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annotate cb_dissimilarity.r @ 2:bcbad4f83dec draft default tip

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planemo upload for repository https://github.com/Marie59/champ_blocs commit 075fd90d1a39ae7912b48549e5537971635b9620
author ecology
date Sat, 18 Mar 2023 16:49:19 +0000
parents 8c6142630659
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8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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1 # author: "Jonathan Richir"
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2 # date: "01 October 2022"
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5 #Rscript
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7 ###############################
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8 ## ##
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9 ###############################
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11 #####Packages : dplyr
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12 # tidyr
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13 # readr
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14 # writexl
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15 # stringr
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16 # readxl
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17 # tibble
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18 # lubridate
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19 # cowplot
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20 # magrittr
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21 # rmarkdown
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22 library(magrittr)
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0
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24 #####Load arguments
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26 args <- commandArgs(trailingOnly = TRUE)
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28 #####Import data
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30 if (length(args) < 1) {
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31 stop("This tool needs at least 1 argument")
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32 }else {
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33 fiche_val <- args[1]
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34 input_data <- args[2]
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35 choice <- args[3]
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36 choice_date <- as.numeric(args[4])
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37 }
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39 #############################################################
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40 # #
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41 # Loading and cleaning data #
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42 # #
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43 #############################################################
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44 # load qecb data
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46 qecb <- read.csv2(input_data, header = TRUE, fileEncoding = "Latin1") # fileEncoding = "Latin1", cfr é in variable names
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48 # import csv files ficheterrain
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50 fiche <- read.csv2(fiche_val, header = TRUE, fileEncoding = "Latin1") # fileEncoding = "Latin1", cfr é in variable names
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52 ## work on "Fiche terrain"
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54 date_fiche <- as.Date(stringr::str_sub(fiche$date.sortie, end = 10), origin = "1970-01-01")
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55 fiche <- tibble::add_column(fiche, date_fiche, .after = "date.sortie")
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56 rm(date_fiche)
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58 ## qecb vs fiche terrain
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60 fiche_red <- dplyr::filter(fiche, fiche$ID.Fiche %in% unique(qecb[, c("id")]))
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62 id_count <- qecb %>% dplyr::group_by(id) %>% dplyr::count()
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63 id_count <- dplyr::rename(id_count, "ID.Fiche" = "id")
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64 id_count <- data.frame(id_count)
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65 fiche_red <- dplyr::left_join(fiche_red, id_count)
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67 # rep fiche terrain information
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68 fiche_expanded <- fiche_red[rep(row.names(fiche_red), fiche_red$n), 1:ncol(fiche_red)]
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69 fiche_expanded <- dplyr::rename(fiche_expanded, "id" = "ID.Fiche")
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71 ## merge qecb data and ficheterrain information
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73 qecb <- dplyr::bind_cols(qecb, fiche_expanded)
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74 qecb <- dplyr::rename(qecb, "id_qecb" = "id...1")
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75 qecb <- dplyr::rename(qecb, "id_fiche" = "id...68")
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77 rm(fiche_expanded, fiche_red, id_count)
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79 qecb <- qecb %>% tidyr::separate(date_fiche, c("Year", "Month", "Day"), sep = "-", remove = FALSE)
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82 ## quadrat nb : in contrast to ivr df, quadrat number is missing for many observations in qecb df ; but from the Numero.Photo variable (boulder photo associated to field data collection), I could get back most missing quadrat numbers
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84 quadrat <- stringr::str_extract(qecb$Numero.Photo, "Q[12345]")
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85 qecb <- tibble::add_column(qecb, quadrat, .after = "Numero.Photo")
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86 rm(quadrat)
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88 # check
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89 quadrat_bis <- rep(NA, length = nrow(qecb))
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90 qecb <- tibble::add_column(qecb, quadrat_bis, .after = "quadrat")
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91 rm(quadrat_bis)
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93 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon %in% c(1, 2) & qecb$Type.Bloc == "Bloc mobile", "Q1", qecb$quadrat_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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94 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon %in% c(3, 4) & qecb$Type.Bloc == "Bloc mobile", "Q2", qecb$quadrat_bis)
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95 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon %in% c(5, 6) & qecb$Type.Bloc == "Bloc mobile", "Q3", qecb$quadrat_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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96 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon %in% c(7, 8) & qecb$Type.Bloc == "Bloc mobile", "Q4", qecb$quadrat_bis)
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97 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon %in% c(9, 10) & qecb$Type.Bloc == "Bloc mobile", "Q5", qecb$quadrat_bis)
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100 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon == 1 & qecb$Type.Bloc %in% c("Bloc fixé", "Roche en place"), "Q1", qecb$quadrat_bis)
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101 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon == 2 & qecb$Type.Bloc %in% c("Bloc fixé", "Roche en place"), "Q2", qecb$quadrat_bis)
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102 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon == 3 & qecb$Type.Bloc %in% c("Bloc fixé", "Roche en place"), "Q3", qecb$quadrat_bis)
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103 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon == 4 & qecb$Type.Bloc %in% c("Bloc fixé", "Roche en place"), "Q4", qecb$quadrat_bis)
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104 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon == 5 & qecb$Type.Bloc %in% c("Bloc fixé", "Roche en place"), "Q5", qecb$quadrat_bis)
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105
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106 ## I create two new variables for Site names, one for data analysis and one for data reporting. Only works for actual ivr df with 22 sites !
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107
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108 # Name for data analysis
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109
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110 qecb <- tibble::add_column(qecb, Site = qecb$zone.habitat, .after = "ID.Fiche")
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111
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112 for (x in seq_along(qecb$Site)) {
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113 if (grepl(pattern = "Locmariaquer", qecb$Site[x]) == TRUE) {
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114 qecb$Site[x] <- "GDMO_Locmariaquer"
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115 } else if (grepl(pattern = "Beg Lann", qecb$Site[x]) == TRUE) {
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116 qecb$Site[x] <- "GDMO_BegLann"
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117 } else if (grepl(pattern = "Plateau du Four", qecb$Site[x]) == TRUE) {
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118 qecb$Site[x] <- "FOUR_PlateauFour"
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119 } else if (grepl(pattern = "Grouin", qecb$Site[x]) == TRUE) {
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120 qecb$Site[x] <- "EGMP_GroinCou"
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121 } else if (grepl(pattern = "Ensembert", qecb$Site[x]) == TRUE) {
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122 qecb$Site[x] <- "EGMP_PasEmsembert"
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123 } else if (grepl(pattern = "Brée-les-Bains", qecb$Site[x]) == TRUE) {
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124 qecb$Site[x] <- "EGMP_BreeBains"
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125 } else if (grepl(pattern = "Antiochat", qecb$Site[x]) == TRUE) {
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126 qecb$Site[x] <- "EGMP_PerreAntiochat"
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127 } else if (grepl(pattern = "Chassiron", qecb$Site[x]) == TRUE) {
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128 qecb$Site[x] <- "EGMP_Chassiron"
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129 } else if (grepl(pattern = "zone p", qecb$Site[x]) == TRUE) {
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130 qecb$Site[x] <- "BASQ_FlotsBleusZP"
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131 } else if (grepl(pattern = "zone f", qecb$Site[x]) == TRUE) {
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132 qecb$Site[x] <- "BASQ_FlotsBleusZF"
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133 } else if (grepl(pattern = "Saint-Michel", qecb$Site[x]) == TRUE) {
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134 qecb$Site[x] <- "GONB_IlotStMichel"
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135 } else if (grepl(pattern = "Quéménès", qecb$Site[x]) == TRUE) {
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136 qecb$Site[x] <- "FINS_Quemenes"
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137 } else if (grepl(pattern = "Goulenez", qecb$Site[x]) == TRUE) {
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138 qecb$Site[x] <- "FINS_SeinGoulenez"
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139 } else if (grepl(pattern = "Kilaourou", qecb$Site[x]) == TRUE) {
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140 qecb$Site[x] <- "FINS_SeinKilaourou"
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141 } else if (grepl(pattern = "Verdelet", qecb$Site[x]) == TRUE) {
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142 qecb$Site[x] <- "ARMO_Verdelet"
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143 } else if (grepl(pattern = "Piégu", qecb$Site[x]) == TRUE) {
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144 qecb$Site[x] <- "ARMO_Piegu"
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145 } else if (grepl(pattern = "Bilfot", qecb$Site[x]) == TRUE) {
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146 qecb$Site[x] <- "ARMO_Bilfot"
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147 } else if (grepl(pattern = "Plate", qecb$Site[x]) == TRUE) {
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148 qecb$Site[x] <- "ARMO_IlePlate"
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149 } else if (grepl(pattern = "Perharidy", qecb$Site[x]) == TRUE) {
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150 qecb$Site[x] <- "PDMO_Perharidy"
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151 } else if (grepl(pattern = "Keraliou", qecb$Site[x]) == TRUE) {
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152 qecb$Site[x] <- "BRES_Keraliou"
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153 } else if (grepl(pattern = "Mousterlin", qecb$Site[x]) == TRUE) {
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154 qecb$Site[x] <- "FINS_Mousterlin"
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155 } else if (grepl(pattern = "Nicolas", qecb$Site[x]) == TRUE) {
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156 qecb$Site[x] <- "FINS_StNicolasGlenan"
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157 }
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158 if (grepl(pattern = "Roz", qecb$site[x]) == TRUE) {
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159 qecb$Site[x] <- "FINS_AnseRoz"
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160 }
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161 }
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162
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163 # Name for report/plot
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164
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165 qecb <- tibble::add_column(qecb, Site_bis = qecb$Site, .after = "Site")
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166
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167 qecb$Site_bis <- ifelse(qecb$Site == "GDMO_Locmariaquer", "Locmariaquer", qecb$Site_bis)
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168 qecb$Site_bis <- ifelse(qecb$Site == "GDMO_BegLann", "Beg Lann", qecb$Site_bis)
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169 qecb$Site_bis <- ifelse(qecb$Site == "FOUR_PlateauFour", "Plateau du Four", qecb$Site_bis)
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170 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_GroinCou", "Groin du Cou", qecb$Site_bis)
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171 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_PasEmsembert", "Le Pas d'Emsembert", qecb$Site_bis)
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172 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_BreeBains", "La Brée-les-Bains", qecb$Site_bis)
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173 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_PerreAntiochat", "Le Perré d'Antiochat", qecb$Site_bis)
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174 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_Chassiron", "Chassiron", qecb$Site_bis)
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175 qecb$Site_bis <- ifelse(qecb$Site == "BASQ_FlotsBleusZP", "Les Flots Bleus / zone pêcheurs", qecb$Site_bis)
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176 qecb$Site_bis <- ifelse(qecb$Site == "BASQ_FlotsBleusZF", "Les Flots Bleus / zone familles", qecb$Site_bis)
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177 qecb$Site_bis <- ifelse(qecb$Site == "GONB_IlotStMichel", "Îlot Saint-Michel", qecb$Site_bis)
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178 qecb$Site_bis <- ifelse(qecb$Site == "FINS_Quemenes", "Quéménès", qecb$Site_bis)
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179 qecb$Site_bis <- ifelse(qecb$Site == "FINS_SeinGoulenez", "Île de Sein - Goulenez", qecb$Site_bis)
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180 qecb$Site_bis <- ifelse(qecb$Site == "FINS_SeinKilaourou", "Île de Sein - Kilaourou", qecb$Site_bis)
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181 qecb$Site_bis <- ifelse(qecb$Site == "ARMO_Verdelet", "Îlot du Verdelet", qecb$Site_bis)
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182 qecb$Site_bis <- ifelse(qecb$Site == "ARMO_Piegu", "Piégu", qecb$Site_bis)
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183 qecb$Site_bis <- ifelse(qecb$Site == "ARMO_Bilfot", "Pointe de Bilfot", qecb$Site_bis)
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184 qecb$Site_bis <- ifelse(qecb$Site == "ARMO_IlePlate", "Île Plate", qecb$Site_bis)
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185 qecb$Site_bis <- ifelse(qecb$Site == "PDMO_Perharidy", "Perharidy", qecb$Site_bis)
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186 qecb$Site_bis <- ifelse(qecb$Site == "BRES_Keraliou", "Keraliou", qecb$Site_bis)
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187 qecb$Site_bis <- ifelse(qecb$Site == "FINS_Mousterlin", "Pointe de Mousterlin", qecb$Site_bis)
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188 qecb$Site_bis <- ifelse(qecb$Site == "FINS_StNicolasGlenan", "Saint-Nicolas des Glénan", qecb$Site_bis)
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189 qecb$Site_bis <- ifelse(qecb$Site == "FINS_AnseRoz", "Pointe de l'Anse du Roz", qecb$Site_bis)
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190
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191 ## change some variables to factor
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192
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193 # change 'X..' variables that are indeed % to numeric; https://stackoverflow.com/questions/59410939/apply-function-to-all-variables-with-string-in-name
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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194 ix <- grep("^X..", names(qecb))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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195 qecb[ix] <- lapply(qecb[ix], as.numeric)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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196 rm(ix)
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197
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198
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199 ## save the final, complete qecb df_
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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200
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201 qecb <- qecb[, c(72:107, 1:71)]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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202
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203 ## qecb df preparation prior qecb calculation
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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204
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205 # Several issues to solve in the df first
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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206
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207
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208 qecb$Type.Bloc <- factor(qecb$Type.Bloc, levels = c("Bloc mobile", "Bloc fixé", "Roche en place"))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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209
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210 qecb$Face <- factor(qecb$Face, levels = c("face supérieure", "face inférieure"))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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211
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212 qecb <- dplyr::arrange(qecb, Type.Bloc, Face, Numéro.Bloc.échantillon)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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213
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214 qecb <- tibble::add_column(qecb, site_year_month_day = paste0(qecb$Site, ".", qecb$Year, ".", qecb$Month, ".", qecb$Day), .after = "Site_bis")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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215
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216 # save qecb as a new df_ for analysis purpose => several changes to operate to run the code and functions
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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217
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218 qecbnew <- qecb
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219
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220 # df with list object nb and corresponding site_year_month_day value to solve for loop issues
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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221
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222 df_list_loop <- data.frame("site_year_month_day" = unique(qecbnew$site_year_month_day),
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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223 "loop nb" = c(1:seq_along(unique(qecbnew$site_year_month_day))))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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224
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225 # dplyr::filter for df that makes problem, then eventually correct in the dataframe for wrong coding; brackets (xx) for nb because will change when qecb df_ enlarged.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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226 # these listed boulder field survey error when highlighted when running the loop, that ran into an error ; it was a step by step procedure with solving one listed observation after another when issues appeared. Surely not the best way to proceed, maybe better just to skip these surveys (site + date), but in the present case I wanted to keep most of the observations, therefore I corrected them manually whenever needed.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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227
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228 # list nb (28) - EGMP_BreeBains.2016.04.06
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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229 qecbnew$Face <- as.character(qecbnew$Face)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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230 qecbnew$Face <- ifelse(qecbnew$ID.Fiche == "BDD_IVR&QECB_La Bree_20160406_VImport.xlsx" & qecbnew$Référence.bloc == "avr16-LaBreeB9sup", "face supérieure", qecbnew$Face)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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231 qecbnew$Face <- ifelse(qecbnew$ID.Fiche == "BDD_IVR&QECB_La Bree_20160406_VImport.xlsx" & qecbnew$Référence.bloc == "avr16-LaBreeB10sup", "face supérieure", qecbnew$Face)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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232 qecbnew$Face <- as.factor(qecbnew$Face)
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233
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234 # list nb 33 - EGMP_PerreAntiochat.2016.04.07
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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235 qecbnew$Face <- as.character(qecbnew$Face)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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236 qecbnew$Face <- ifelse(qecbnew$ID.Fiche == "BDD_IVR&QECB_PerAnt_20160407_VImport.xlsx" & qecbnew$Référence.bloc == "avr16-PerAntB9sup", "face supérieure", qecbnew$Face)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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237 qecbnew$Face <- ifelse(qecbnew$ID.Fiche == "BDD_IVR&QECB_PerAnt_20160407_VImport.xlsx" & qecbnew$Référence.bloc == "avr16-PerAntB10sup", "face supérieure", qecbnew$Face)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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238 qecbnew$Face <- as.factor(qecbnew$Face)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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239
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240 # list nb 37 - EGMP_Chassiron.2016.03.09
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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241 qecbnew$Face <- as.character(qecbnew$Face)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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242 qecbnew$Face <- ifelse(qecbnew$ID.Fiche == "BDD_IVR&QECB_Chassiron_20160309&10_VImport.xlsx" & qecbnew$Référence.bloc == "mars16-ChassB9sup", "face supérieure", qecbnew$Face)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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243 qecbnew$Face <- ifelse(qecbnew$ID.Fiche == "BDD_IVR&QECB_Chassiron_20160309&10_VImport.xlsx" & qecbnew$Référence.bloc == "mars16-ChasB10sup", "face supérieure", qecbnew$Face)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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244 qecbnew$Face <- as.factor(qecbnew$Face)
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245
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246 # list nb 76 - ARMO_Verdelet.2015.03.23
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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247 qecbnew$Face <- as.character(qecbnew$Face)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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248 qecbnew$Face <- ifelse(qecbnew$ID.Fiche == "BDD_IVR&QECB_Verdelet_20150323_VImport.xlsx" & qecbnew$Référence.bloc == "mar15-VerB10inf", "face inférieure", qecbnew$Face)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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249 qecbnew$Face <- as.factor(qecbnew$Face)
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250
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251 # list nb 116 - "GDMO_Locmariaquer.2018.09.10"
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252 qecbnew$Type.Bloc <- as.character(qecbnew$Type.Bloc)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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253 qecbnew$Type.Bloc <- ifelse(qecbnew$ID.Fiche == "2018-09-10-GDMO-CDB-001" & qecbnew$Numero.Photo == "2018-09-10_GDMO_01_CDB-5_sup_392578.jpg", "Roche en place", qecbnew$Type.Bloc)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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254 qecbnew$Type.Bloc <- as.factor(qecbnew$Type.Bloc)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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255 qecbnew$quadrat_bis <- ifelse(qecbnew$ID.Fiche == "2018-09-10-GDMO-CDB-001" & qecbnew$Numero.Photo == "2018-09-10_GDMO_01_CDB-5_sup_392578.jpg", "Q5", qecbnew$quadrat_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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256 qecbnew <- qecbnew %>% dplyr::filter(!(ID.Fiche == "2018-09-10-GDMO-CDB-001" & Numero.Photo == ""))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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257
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258 # Few sites to remove prior running the for loop because it was not just a encoding mistake for one data, but a globally wroing coding for the site + date survey.
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259
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260 qecb_i <- qecbnew %>% dplyr::filter(site_year_month_day == "FINS_StNicolasGlenan.2016.04.08") # no bloc fixe !
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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261 qecbnew <- qecbnew %>% dplyr::filter(site_year_month_day != "FINS_StNicolasGlenan.2016.04.08")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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262 qecb_i <- qecbnew %>% dplyr::filter(site_year_month_day == "GDMO_Locmariaquer.2019.09.30") # most faces of blocs mobiles do not correspond to each other; only 3 over 10 boulder have data for both face supérieure and face inférieure
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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263 qecbnew <- qecbnew %>% dplyr::filter(site_year_month_day != "GDMO_Locmariaquer.2019.09.30")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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264 rm(df_list_loop, qecb_i)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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265
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266
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267 # check for species with count within sub-0.1m^2-quadrat (i.e. reduced size quadrat compare to most organisms on boulder to count them, because abundant ; then some extrapolation)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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268
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269 # first for Spirobranchus
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270
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271 qecbnew$Nb.Spirobranchus.lamarckii.total.ini <- qecbnew$Nb.Spirobranchus.lamarckii.total
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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272 qecbnew$Nb.Spirobranchus.lamarckii.total <- as.character(qecbnew$Nb.Spirobranchus.lamarckii.total)
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273
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274
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275 qecbnew_spirobranchus <- (dplyr::filter(qecbnew, Nb.Spirobranchus.lamarckii.total %in% c(NA, "NaN", "Inf", "-Inf")))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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276 qecbnew_spirobranchus[, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B")] <- sapply(qecbnew_spirobranchus[, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B")], as.character)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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277 (spirobranchus_data <- subset(qecbnew_spirobranchus, !is.na(qecbnew_spirobranchus$Nb.Spirobranchus.lamarckii.1B) || !is.na(qecbnew_spirobranchus$Nb.Spirobranchus.lamarckii.2B) || !is.na(qecbnew_spirobranchus$Nb.Spirobranchus.lamarckii.3B) || !is.na(qecbnew_spirobranchus$Nb.Spirobranchus.lamarckii.4B) || !is.na(qecbnew_spirobranchus$Nb.Spirobranchus.lamarckii.5B))[, c("site_year_month_day", "Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total")])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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278
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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279 quemenes <- dplyr::filter(qecbnew, Site == "FINS_Quemenes")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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280 quemenes <- dplyr::arrange(quemenes, date_fiche)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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281 # for Quemenes, issue because for sampling date "FINS_Quemenes.2015.09.30" the 5 counts of Spirobranchus were encoded in 1B instead of total !!! I noticed this issue when mining data (see below), therefore I corrected before running below script for Spirobranchus.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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282 qecbnew$Nb.Spirobranchus.lamarckii.total <- ifelse(qecbnew$site_year_month_day == "FINS_Quemenes.2015.09.30" & is.na(qecbnew$Nb.Spirobranchus.lamarckii.total), qecbnew$Nb.Spirobranchus.lamarckii.1B, qecbnew$Nb.Spirobranchus.lamarckii.total)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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283
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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284 (quemenes <- dplyr::filter(qecbnew, site_year_month_day == "FINS_Quemenes.2015.09.30")[, c("site_year_month_day", "Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total")])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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285 rm(quemenes)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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286
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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287 seinkilaourou <- dplyr::filter(qecbnew, Site == "FINS_SeinKilaourou")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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288 seinkilaourou <- dplyr::arrange(seinkilaourou, date_fiche)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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289 # same issue with SeinKilaourou
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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290 qecbnew$Nb.Spirobranchus.lamarckii.total <- ifelse(qecbnew$site_year_month_day == "FINS_SeinKilaourou.2015.04.21" & is.na(qecbnew$Nb.Spirobranchus.lamarckii.total), qecbnew$Nb.Spirobranchus.lamarckii.1B, qecbnew$Nb.Spirobranchus.lamarckii.total)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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291 (seinkilaourou <- dplyr::filter(qecbnew, site_year_month_day == "FINS_SeinKilaourou.2015.04.21")[, c("site_year_month_day", "Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total")])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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292 rm(seinkilaourou)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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293
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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294 # some more issues however with "x100"count data
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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295 spirobranchus <- subset(qecbnew, !is.na(qecbnew$Nb.Spirobranchus.lamarckii.1B) & !is.na(qecbnew$Nb.Spirobranchus.lamarckii.2B) & !is.na(qecbnew$Nb.Spirobranchus.lamarckii.3B) & !is.na(qecbnew$Nb.Spirobranchus.lamarckii.4B) & !is.na(qecbnew$Nb.Spirobranchus.lamarckii.5B) & !is.na(qecbnew$Nb.Spirobranchus.lamarckii.total))[, c("site_year_month_day", "Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total")]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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296
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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297 for (i in c(1:nrow(spirobranchus))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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298 spirobranchus$mean.x.100[[i]] <- sum(spirobranchus[i, c(2:6)], na.rm = TRUE) / sum(!is.na(spirobranchus[i, c(2:6)])) * 100
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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299 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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300
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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301 spirobranchus$mean.x.100 <- unlist(spirobranchus$mean.x.100)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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302 spirobranchus$Nb.Spirobranchus.lamarckii.total <- as.numeric(spirobranchus$Nb.Spirobranchus.lamarckii.total)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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303 for (i in c(1:nrow(spirobranchus))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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304 spirobranchus$diff[[i]] <- spirobranchus[i, "Nb.Spirobranchus.lamarckii.total"] - spirobranchus[i, "mean.x.100"]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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305 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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306
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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307 spirobranchus$diff <- abs(as.integer(spirobranchus$diff))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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308 spirobranchus <- dplyr::arrange(spirobranchus, desc(diff), mean.x.100)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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309 spirobranchus <- dplyr::arrange(dplyr::filter(spirobranchus, diff != 0 & mean.x.100 != 0), desc(diff))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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310
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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311 # check it all in the qecbnew df
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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312
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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313 for (i in c(1:nrow(qecbnew))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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314 qecbnew$mean.x.100[[i]] <-
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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315 sum(qecbnew[i, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B")], na.rm = TRUE) / sum(!is.na(qecbnew[i, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B")])) * 100
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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316 } # sum of only NAs/0 = NaN; so replace NaN by Na
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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317 qecbnew$mean.x.100 <- as.character(qecbnew$mean.x.100)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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318
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319
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320 for (i in c(1:nrow(qecbnew))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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321 qecbnew$mean.x.100[[i]] <- ifelse(qecbnew$mean.x.100[[i]] == "NaN", NA, qecbnew$mean.x.100[[i]])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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322 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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323 qecbnew$mean.x.100 <- as.integer(qecbnew$mean.x.100)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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324
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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325 qecbnew$Nb.Spirobranchus.lamarckii.total <- as.integer(qecbnew$Nb.Spirobranchus.lamarckii.total)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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326 qecbnew$Nb.Spirobranchus.lamarckii.total.diff <- abs((qecbnew$Nb.Spirobranchus.lamarckii.total - qecbnew$mean.x.100))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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327 spirobranchus_diff <- qecbnew[, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total", "Nb.Spirobranchus.lamarckii.total.ini", "mean.x.100", "Nb.Spirobranchus.lamarckii.total.diff")]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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328 spirobranchus_diff <- dplyr::arrange(spirobranchus_diff, desc(Nb.Spirobranchus.lamarckii.total.diff), mean.x.100)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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329 spirobranchus_diff <- dplyr::arrange(dplyr::filter(spirobranchus_diff, Nb.Spirobranchus.lamarckii.total.diff != 0 & mean.x.100 != 0), desc(Nb.Spirobranchus.lamarckii.total.diff))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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330
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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331 qecbnew$Nb.Spirobranchus.lamarckii.total <- ifelse(qecbnew$Nb.Spirobranchus.lamarckii.total.diff != 0 & qecbnew$mean.x.100 != 0, qecbnew$mean.x.100, qecbnew$Nb.Spirobranchus.lamarckii.total)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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332 spirobranchus_diff <- qecbnew[, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total", "Nb.Spirobranchus.lamarckii.total.ini", "mean.x.100", "Nb.Spirobranchus.lamarckii.total.diff")]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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333 spirobranchus_diff$Nb.Spirobranchus.lamarckii.total.diff <- abs(as.integer(spirobranchus_diff$Nb.Spirobranchus.lamarckii.total.diff))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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diff changeset
334 spirobranchus_diff <- dplyr::arrange(spirobranchus_diff, desc(Nb.Spirobranchus.lamarckii.total.diff), mean.x.100)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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diff changeset
335 spirobranchus_diff <- dplyr::arrange(dplyr::filter(spirobranchus_diff, Nb.Spirobranchus.lamarckii.total.diff != 0 & mean.x.100 != 0), desc(Nb.Spirobranchus.lamarckii.total.diff))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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336 # ok, change made when data x 100 was not correct.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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337
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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338 # finally, change NA by mean.x100 for Spirobranchus total
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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339 qecbnew$Nb.Spirobranchus.lamarckii.total <- as.character(qecbnew$Nb.Spirobranchus.lamarckii.total)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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340 for (i in c(1:nrow(qecbnew))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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341 qecbnew$Nb.Spirobranchus.lamarckii.total[[i]] <- ifelse(qecbnew$Nb.Spirobranchus.lamarckii.total[[i]] %in% c(NA, "NaN", "Inf", "-Inf"), sum(qecbnew[i, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B")], na.rm = TRUE) / sum(!is.na(qecbnew[i, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B")])) * 100, qecbnew$Nb.Spirobranchus.lamarckii.total[[i]])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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342 } # sum of only NAs/0 = NaN; so replace NaN by Na
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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343
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344
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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diff changeset
345 for (i in c(1:nrow(qecbnew))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
346 qecbnew$Nb.Spirobranchus.lamarckii.total[[i]] <- ifelse(qecbnew$Nb.Spirobranchus.lamarckii.total[[i]] == "NaN", NA, qecbnew$Nb.Spirobranchus.lamarckii.total[[i]])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
347 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
348
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
349 qecbnew$Nb.Spirobranchus.lamarckii.total <- as.integer(qecbnew$Nb.Spirobranchus.lamarckii.total)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
350
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
351 qecbnew$Nb.Spirobranchus.lamarckii.total.diff <- abs(qecbnew$Nb.Spirobranchus.lamarckii.total - qecbnew$Nb.Spirobranchus.lamarckii.total.ini)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
352 spirobranchus_diff <- qecbnew[, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total", "Nb.Spirobranchus.lamarckii.total.ini", "mean.x.100", "Nb.Spirobranchus.lamarckii.total.diff")]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
353 spirobranchus_diff <- dplyr::arrange(spirobranchus_diff, desc(Nb.Spirobranchus.lamarckii.total.diff), mean.x.100)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
354 spirobranchus_diff <- dplyr::arrange(dplyr::filter(spirobranchus_diff, Nb.Spirobranchus.lamarckii.total.diff != 0 & mean.x.100 != 0), desc(Nb.Spirobranchus.lamarckii.total.diff))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
355
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
356 qecbnew <- subset(qecbnew, select = -c(Nb.Spirobranchus.lamarckii.total.ini, mean.x.100, Nb.Spirobranchus.lamarckii.total.diff))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
357
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
358 rm(qecbnew_spirobranchus, spirobranchus, spirobranchus_data, spirobranchus_diff)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
359
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
360 # do the same for spirorbis
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
361
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
362 qecbnew$Nb.spirorbis.total.ini <- qecbnew$Nb.spirorbis.total
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
363 qecbnew$Nb.spirorbis.total <- as.character(qecbnew$Nb.spirorbis.total)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
364
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
365 qecbnew_spirorbis <- (dplyr::filter(qecbnew, Nb.spirorbis.total %in% c(NA, "NaN", "Inf", "-Inf")))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
366 qecbnew_spirorbis[, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A")] <- sapply(qecbnew_spirorbis[, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A")], as.character)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
367 (spirobranchus_data <- subset(qecbnew_spirorbis, !is.na(qecbnew_spirorbis$Nb.spirorbis.1A) || !is.na(qecbnew_spirorbis$Nb.spirorbis.2A) || !is.na(qecbnew_spirorbis$Nb.spirorbis.3A) || !is.na(qecbnew_spirorbis$Nb.spirorbis.4A) || !is.na(qecbnew_spirorbis$Nb.spirorbis.5A))[, c("site_year_month_day", "Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A", "Nb.spirorbis.total")])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
368
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
369 # In contrast to Spirobranchus data, no encoding issues for spirorbis data, cfr when sub-quadrat 1A-5A are ALL encoded, NA for total.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
370
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
371 # some more issues however with "x200"count data
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
372
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
373 spirorbis <- subset(qecbnew, !is.na(qecbnew$Nb.spirorbis.1A) & !is.na(qecbnew$Nb.spirorbis.2A) & !is.na(qecbnew$Nb.spirorbis.3A) & !is.na(qecbnew$Nb.spirorbis.4A) & !is.na(qecbnew$Nb.spirorbis.5A) & !is.na(qecbnew$Nb.spirorbis.total))[, c("site_year_month_day", "Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A", "Nb.spirorbis.total")]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
374 for (i in c(1:nrow(spirorbis))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
375 spirorbis$mean.x.200[[i]] <- sum(spirorbis[i, c(2:6)], na.rm = TRUE) / sum(!is.na(spirorbis[i, c(2:6)])) * 200
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
376 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
377 spirorbis$mean.x.200 <- unlist(spirorbis$mean.x.200)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
378 spirorbis$Nb.spirorbis.total <- as.numeric(spirorbis$Nb.spirorbis.total)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
379 for (i in c(1:nrow(spirorbis))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
380 spirorbis$diff[[i]] <- spirorbis[i, "Nb.spirorbis.total"] - spirorbis[i, "mean.x.200"]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
381 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
382 spirorbis$diff <- abs(as.integer(spirorbis$diff))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
383 spirorbis <- dplyr::arrange(spirorbis, desc(diff), mean.x.200)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
384 (gonb_ilotstmichel_2015_04_18 <- dplyr::filter(spirorbis, site_year_month_day == "GONB_IlotStMichel.2015.04.18"))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
385 rm(gonb_ilotstmichel_2015_04_18)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
386 spirorbis <- dplyr::arrange(dplyr::filter(spirorbis, diff != 0 & mean.x.200 != 0), desc(diff))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
387
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
388 # check it all in the qecbnew df
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
389
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
390 for (i in c(1:nrow(qecbnew))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
391 qecbnew$mean.x.200[[i]] <- sum(qecbnew[i, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A")], na.rm = TRUE) / sum(!is.na(qecbnew[i, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A")])) * 200
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
392 } # sum of only NAs/0 = NaN; so replace NaN by Na
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
393 qecbnew$mean.x.200 <- as.character(qecbnew$mean.x.200)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
394
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
395 for (i in c(1:nrow(qecbnew))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
396 qecbnew$mean.x.200[[i]] <- ifelse(qecbnew$mean.x.200[[i]] == "NaN", NA, qecbnew$mean.x.200[[i]])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
397 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
398
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
399 qecbnew$mean.x.200 <- as.integer(qecbnew$mean.x.200)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
400
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
401 qecbnew$Nb.spirorbis.total <- as.integer(qecbnew$Nb.spirorbis.total)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
402 qecbnew$Nb.spirorbis.total.diff <- abs((qecbnew$Nb.spirorbis.total - qecbnew$mean.x.200))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
403 spirorbis_diff <- qecbnew[, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A", "Nb.spirorbis.total", "Nb.spirorbis.total.ini", "mean.x.200", "Nb.spirorbis.total.diff")]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
404 spirorbis_diff <- dplyr::arrange(spirorbis_diff, desc(Nb.spirorbis.total.diff), mean.x.200)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
405 spirorbis_diff <- dplyr::arrange(dplyr::filter(spirorbis_diff, Nb.spirorbis.total.diff != 0 & mean.x.200 != 0), desc(Nb.spirorbis.total.diff))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
406
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
407 qecbnew$Nb.spirorbis.total <- ifelse(qecbnew$Nb.spirorbis.total.diff != 0 & qecbnew$mean.x.200 != 0, qecbnew$mean.x.200, qecbnew$Nb.spirorbis.total)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
408 spirorbis_diff <- qecbnew[, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A", "Nb.spirorbis.total", "Nb.spirorbis.total.ini", "mean.x.200", "Nb.spirorbis.total.diff")]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
409 spirorbis_diff$Nb.spirorbis.total.diff <- abs(as.integer(spirorbis_diff$Nb.spirorbis.total.diff))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
410 spirorbis_diff <- dplyr::arrange(spirorbis_diff, desc(Nb.spirorbis.total.diff), mean.x.200)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
411 spirorbis_diff <- dplyr::arrange(dplyr::filter(spirorbis_diff, Nb.spirorbis.total.diff != 0 & mean.x.200 != 0), desc(Nb.spirorbis.total.diff))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
412 # ok, change made when data x 200 was not correct.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
413
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
414 # finally, change NA by mean.x200 for spirorbis total
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
415 qecbnew$Nb.spirorbis.total <- as.character(qecbnew$Nb.spirorbis.total)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
416 for (i in c(1:nrow(qecbnew))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
417 qecbnew$Nb.spirorbis.total[[i]] <- ifelse(qecbnew$Nb.spirorbis.total[[i]] %in% c(NA, "NaN", "Inf", "-Inf"), sum(qecbnew[i, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A")], na.rm = TRUE) / sum(!is.na(qecbnew[i, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A")])) * 200, qecbnew$Nb.spirorbis.total[[i]])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
418 } # sum of only NAs/0 = NaN; so replace NaN by Na
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
419
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
420 for (i in c(1:nrow(qecbnew))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
421 qecbnew$Nb.spirorbis.total[[i]] <- ifelse(qecbnew$Nb.spirorbis.total[[i]] == "NaN", NA, qecbnew$Nb.spirorbis.total[[i]])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
422 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
423
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
424 qecbnew$Nb.spirorbis.total <- as.integer(qecbnew$Nb.spirorbis.total)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
425
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
426 qecbnew$Nb.spirorbis.total.diff <- abs(qecbnew$Nb.spirorbis.total - qecbnew$Nb.spirorbis.total.ini)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
427 spirorbis_diff <- qecbnew[, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A", "Nb.spirorbis.total", "Nb.spirorbis.total.ini", "mean.x.200", "Nb.spirorbis.total.diff")]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
428 spirorbis_diff <- dplyr::arrange(spirorbis_diff, desc(Nb.spirorbis.total.diff), mean.x.200)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
429 spirorbis_diff <- dplyr::arrange(dplyr::filter(spirorbis_diff, Nb.spirorbis.total.diff != 0 & mean.x.200 != 0), desc(Nb.spirorbis.total.diff))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
430
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
431 qecbnew <- subset(qecbnew, select = -c(Nb.spirorbis.total.ini, mean.x.200, Nb.spirorbis.total.diff))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
432
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
433 rm(qecbnew_spirorbis, spirorbis, spirobranchus_data, spirorbis_diff, i)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
434
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
435
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
436 # dplyr::filter for abnormal data, based on histogram distribution of data
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
437
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
438 dplyr::filter(qecbnew, X..algues.brunes > 100)[, c("Site", "date_fiche", "Type.Bloc", "Numéro.Bloc.échantillon", "Face", "X..algues.brunes")]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
439 qecbnew$X..algues.brunes <- ifelse(qecbnew$X..algues.brunes > 100, 100, qecbnew$X..algues.brunes)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
440 dplyr::filter(qecbnew, X..algues.rouges > 100)[, c("Site", "date_fiche", "Type.Bloc", "Numéro.Bloc.échantillon", "Face", "X..algues.rouges")]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
441 qecbnew$X..algues.rouges <- ifelse(qecbnew$X..algues.rouges > 100, 100, qecbnew$X..algues.rouges)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
442
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
443
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
444 ## SCRIPT I - NAs <- 0 ; cfr previous comment makes no sense to have NA encoded when the presence of an organism is in reality = 0
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
445
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
446 # We are facing an issues with NA observations, because either they were not measured/counted, then they are effectively NAs; or these NAs = indeed "0"; but I cannot have NAs for variables that are included in the index determination, cfr if 5+0 = 5, 5+NA = NA; see for example site_year_month_day == "ARMO_Bilfot.2014.04.28", Nb.Spirobranchus.lamarckii.total is NA ...
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
447 # I theregore change these NAs by 0
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
448
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
449 # replace NAs by "0" for variables used in qecb determination
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
450 qecbnew[, c("X..algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
451 "X..algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
452 "X..Lithophyllum",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
453 "X..Cladophora",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
454 "Nb.Littorina.obtusata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
455 "Nb.Gibbula.cineraria",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
456 "Nb.Gibbula.pennanti",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
457 "Nb.Gibbula.umbilicalis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
458 "X..Eponges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
459 "X..Ascidies.Coloniales",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
460 "X..Ascidies.Solitaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
461 "X..Bryozoaires.Dresses",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
462 "X..algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
463 "X..Roche.Nue",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
464 "Nb.spirorbis.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
465 "X..Balanes.Vivantes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
466 "Nb.Spirobranchus.lamarckii.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
467 "X..Surface.Accolement")] <- lapply(qecbnew[,
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
468 c("X..algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
469 "X..algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
470 "X..Lithophyllum",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
471 "X..Cladophora",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
472 "Nb.Littorina.obtusata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
473 "Nb.Gibbula.cineraria",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
474 "Nb.Gibbula.pennanti",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
475 "Nb.Gibbula.umbilicalis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
476 "X..Eponges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
477 "X..Ascidies.Coloniales",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
478 "X..Ascidies.Solitaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
479 "X..Bryozoaires.Dresses",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
480 "X..algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
481 "X..Roche.Nue",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
482 "Nb.spirorbis.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
483 "X..Balanes.Vivantes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
484 "Nb.Spirobranchus.lamarckii.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
485 "X..Surface.Accolement")],
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
486 function(x) replace(x, is.na(x), 0))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
487
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
488 # and also replace NA for bivalve by 0 for EGMP and BASQ surveys cfr for accollement correction later on.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
489
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
490 qecbnew$X..Mytilus.sp. <- ifelse((substr(qecbnew$Site, 1, 4) %in% c("EGMP", "BASQ")) & is.na(qecbnew$X..Mytilus.sp.), 0, qecbnew$X..Mytilus.sp.)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
491 qecbnew$Nb.Crassostrea.gigas <- ifelse((substr(qecbnew$Site, 1, 4) %in% c("EGMP", "BASQ")) & is.na(qecbnew$Nb.Crassostrea.gigas), 0, qecbnew$Nb.Crassostrea.gigas)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
492 qecbnew$Nb.Ostrea.edulis <- ifelse((substr(qecbnew$Site, 1, 4) %in% c("EGMP", "BASQ")) & is.na(qecbnew$Nb.Ostrea.edulis), 0, qecbnew$Nb.Ostrea.edulis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
493
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
494
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
495 # add a region variable
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
496 region <- rep(NA, nrow(qecbnew))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
497 qecbnew <- tibble::add_column(qecbnew, region, .after = "Site_bis")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
498 qecbnew$region <- ifelse(qecbnew$Site %in% c("EGMP_GroinCou", "EGMP_PasEmsembert", "EGMP_BreeBains", "EGMP_PerreAntiochat", "EGMP_Chassiron", "BASQ_FlotsBleusZP", "BASQ_FlotsBleusZF"), "EGMP.BASQ", "Bretagne")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
499 rm(region)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
500 qecbnew <- dplyr::arrange(qecbnew, region, site_year_month_day, Type.Bloc, Numéro.Bloc.échantillon, Face)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
501
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
502 # accolement function according to recent 'retournement'
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
503
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
504 ## before I go further ahead, I have to correct for surface d'accollement for several variable for BM.FI !!
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
505
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
506 # not the same file name between script qecb script (qecbNew) and this script (qecbNew); doesn't matter, only appears here in the first dplyr::filter lines.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
507
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
508 qecbnew <- tibble::add_column(qecbnew, terri_ = substr(qecbnew$Site, 1, 4), .after = "Site_bis")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
509
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
510 qecbnew$X..Eponges_ini <- qecbnew$X..Eponges
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
511 qecbnew$X..Ascidies.Coloniales_ini <- qecbnew$X..Ascidies.Coloniales
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
512 qecbnew$X..Ascidies.Solitaires_ini <- qecbnew$X..Ascidies.Solitaires
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
513 qecbnew$X..Bryozoaires.Dresses_ini <- qecbnew$X..Bryozoaires.Dresses
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
514 qecbnew$X..Lithophyllum_ini <- qecbnew$X..Lithophyllum
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
515 qecbnew$X..Balanes.Vivantes_ini <- qecbnew$X..Balanes.Vivantes
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
516
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
517 df_bm_fs <- qecbnew %>% dplyr::filter(Type.Bloc == "Bloc mobile" & Face == "face supérieure")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
518 df_bm_fi <- qecbnew %>% dplyr::filter(Type.Bloc == "Bloc mobile" & Face == "face inférieure")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
519 df_bf <- qecbnew %>% dplyr::filter(Type.Bloc != "Bloc mobile")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
520
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
521 `%notin%` <- Negate(`%in%`)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
522
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
523 acco_fct <- function(var_) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
524
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
525 df_bm_fi$var_cor.acco. <<- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
526
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
527 for (i in c(1:nrow(df_bm_fi))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
528
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
529 df_bm_fi$var_cor.acco.[[i]] <<- if (df_bm_fi$terri_[[i]] %notin% c("EGMP", "BASQ")) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
530 ifelse(#df_$Couleur.dominante %in% c("Rouge", "Brune", "Brune-Rouge") ||
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
531 df_bm_fs$Couleur.dominante[[i]] %in% c("Blanche", "Verte", "Blanche-Verte", "Colorée"), df_bm_fi[i, var_] / (100 - df_bm_fi$X..Surface.Accolement[[i]]) * 100, df_bm_fi[i, var_])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
532 } else {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
533 ifelse(df_bm_fs$Couleur.dominante[[i]] %in% c("Blanche", "Verte", "Blanche-Verte", "Colorée")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
534 & df_bm_fi$X..Surface.Accolement[[i]] != 0 # I have to use it in dplyr::filter this time as well for EGMP- BASQ (but not for Bretagne, although could be added, same result); identical/repeated measure for BM.FI and BM.FS
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
535 & df_bm_fs$X..Mytilus.sp.[[i]] == 0, df_bm_fi[i, var_] / (100 - df_bm_fi$X..Surface.Accolement[[i]]) * 100, df_bm_fi[i, var_])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
536 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
537
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
538 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
539
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
540 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
541
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
542 # I would only consider colors in c("Rouge", "Brune", "Brune-Rouge") for BM.FI correction [ and not the series c("Blanche-Brune", "Rouge", "Brune", "Blanche-Rouge", "Brune-Rouge", "Rouge-Verte", "Brune-Verte") ] ; and for BM.FS, the list c("Blanche", "Verte", "Colorée") => we do the correction for BM.FI accollement based on BM.FS color !!!
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
543
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
544
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
545 # apply acco_fct to BM.FI variables
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
546
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
547 apply_acco_fct <- function(var_) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
548
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
549 show(sort(df_bm_fi[, var_], decreasing = TRUE, index.return = FALSE)[1:50])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
550 pre_ <- as.vector(df_bm_fi[, var_])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
551 acco_fct(var_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
552 df_bm_fi <<- tibble::add_column(df_bm_fi, var_cor. = df_bm_fi$var_cor.acco., .after = var_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
553 show(sort(df_bm_fi$var_cor., decreasing = TRUE, index.return = FALSE)[1:50])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
554 df_bm_fi$var_cor. <<- as.numeric(ifelse(as.character(df_bm_fi$var_cor.) %in% c(NA, "NaN", "-Inf", "Inf"), "0", as.character(df_bm_fi$var_cor.)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
555 df_bm_fi$var_cor. <<- ifelse(df_bm_fi$var_cor. > 100, 100, df_bm_fi$var_cor.)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
556 show(sort(df_bm_fi$var_cor., decreasing = TRUE, index.return = FALSE)[1:50])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
557 show(length(na.omit(which(abs(as.vector(df_bm_fi$var_cor.) - pre_) != 0))) / na.omit(length(df_bm_fi$var_cor.)) * 100)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
558 par(mfrow = c(1, 3))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
559 hist(pre_, main = var_, xlab = "pre-corection")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
560 hist(df_bm_fi$var_cor., main = var_, xlab = "post-corection")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
561 hist(df_bm_fi[as.vector(which(abs(as.vector(df_bm_fi$var_cor.) - pre_) != 0)), var_], main = var_, xlab = "diff. post-pre != 0")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
562 par(mfrow = c(1, 1))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
563 df_bm_fi <<- df_bm_fi[, -which(names(df_bm_fi) %in% c(var_, "var_cor.acco."))]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
564 colnames(df_bm_fi)[colnames(df_bm_fi) == "var_cor."] <<- var_
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
565
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
566 rm(pre_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
567
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
568 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
569
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
570 apply_acco_fct("X..Eponges")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
571 apply_acco_fct("X..Ascidies.Coloniales")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
572 apply_acco_fct("X..Ascidies.Solitaires")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
573 apply_acco_fct("X..Bryozoaires.Dresses")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
574 apply_acco_fct("X..Lithophyllum")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
575 apply_acco_fct("X..Balanes.Vivantes")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
576
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
577 qecbnew <- dplyr::bind_rows(df_bm_fs, df_bm_fi)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
578 qecbnew <- dplyr::bind_rows(qecbnew, df_bf)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
579
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
580 qecbnew <- dplyr::arrange(qecbnew, region, site_year_month_day, Type.Bloc, Numéro.Bloc.échantillon, Face)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
581
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
582 # do remove some more data ...
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
583 # "FINS_Quemenes.2020.10.16", bad encoding, I let know Anna Capietto to make changes => was corrected normally, so unactivate next time I download ESTAMP data
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
584 qecbnew <- dplyr::filter(qecbnew, site_year_month_day != "FINS_Quemenes.2020.10.16")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
585
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
586 # save the final qecbnew df_
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
587
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
588 qecb <- qecbnew
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
589
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
590
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
591 `%notin%` <- Negate(`%in%`)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
592
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
593 ## reorder and/or create new variables
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
594
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
595 # variable site_year_month_day moved for clarity purpose, not needed necessarily
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
596 qecb <- tibble::add_column(qecb, qecb$site_year_month_day, .after = "Site_bis")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
597 qecb <- qecb[, -which(names(qecb) %in% c("site_year_month_day"))]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
598 qecb <- dplyr::rename(qecb, site_year_month_day = `qecb$site_year_month_day`)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
599
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
600 # new variable period (nothing to see with the existing périod variable)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
601 period <- rep(NA, nrow(qecb))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
602 qecb <- tibble::add_column(qecb, period, .after = "Day")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
603 qecb$period <- ifelse(as.numeric(qecb$Month) < 7, "p1", "p2")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
604 qecb$period <- as.factor(qecb$period)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
605 rm(period)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
606
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
607 qecb <- dplyr::arrange(qecb, region, site_year_month_day, Type.Bloc, Numéro.Bloc.échantillon, Face)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
608
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
609 # NB: les infos surface d'accolement sont dupliquées de la face inf vers la face sup de blocs mobiles (même si peu de sens d'avoir cette info pour les face sup ...)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
610 # NB: les data "Abondance ressources ciblées par pêcheurs à pied" présentes uniquement pour les blocs mobiles sont dupliquées entre face inf et face sup.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
611
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
612 ## SCRIPT I - NAs <- 0
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
613
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
614 # already performed for part in the CB_qecb script ; but here I also consider mobile organisms, logical observation (or not) according to boulders, faces etc ... so more complete. Could be some kind of script fusion to only keep Na to 0 correction in one script, i.e. moving this script to the CB_qecb script ...
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
615
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
616 bretagne_bm <- dplyr::filter(qecb, region == "Bretagne" & Type.Bloc == "Bloc mobile")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
617 bretagne_bf <- dplyr::filter(qecb, region == "Bretagne" & Type.Bloc %in% c("Bloc fixé", "Roche en place"))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
618 egmp_basq_bm <- dplyr::filter(qecb, region == "EGMP.BASQ" & Type.Bloc == "Bloc mobile")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
619 egmp_basq_bf <- dplyr::filter(qecb, region == "EGMP.BASQ" & Type.Bloc %in% c("Bloc fixé", "Roche en place"))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
620
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
621 # replace NAs by "0" for variables used in qecb determination
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
622
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
623 bretagne_bm[, c(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
624 "X..algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
625 "Strate.algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
626 "X..algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
627 "Strate.algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
628 "X..algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
629 "Strate.algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
630 "X..Cladophora",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
631 "X..Lithophyllum",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
632 "X..Recouvrement.Sediment", # is NA, then replace by 0 as well because no sense to have a NA value for "% recouvrement sédiment" as well.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
633 #"Type.Sediment",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
634 "X..Roche.Nue", # is NA, then replace by 0 as well because no sense to have a NA value for "% roche nue" as well.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
635 "Nb.Littorina.obtusata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
636 "Nb.Gibbula.cineraria",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
637 "Nb.Gibbula.pennanti",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
638 "Nb.Gibbula.umbilicalis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
639 "Nb.Phallusia.mamillata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
640 "Nb.Tethya.aurantium",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
641 #"Nb.Spirobranchus.lamarckii.1B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
642 #"Nb.Spirobranchus.lamarckii.2B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
643 #"Nb.Spirobranchus.lamarckii.3B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
644 #"Nb.Spirobranchus.lamarckii.4B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
645 #"Nb.Spirobranchus.lamarckii.5B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
646 "Nb.Spirobranchus.lamarckii.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
647 #"Nb.spirorbis.1A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
648 #"Nb.spirorbis.2A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
649 #"Nb.spirorbis.3A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
650 #"Nb.spirorbis.4A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
651 #"Nb.spirorbis.5A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
652 "Nb.spirorbis.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
653 #.."Nb.Crassostrea.gigas",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
654 #.."Nb.Ostrea.edulis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
655 #.."X..Mytilus.sp.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
656 #.."X..Hermelles",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
657 #.."X..Hydraires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
658 "X..Eponges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
659 "X..Ascidies.Coloniales",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
660 "X..Ascidies.Solitaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
661 "X..Bryozoaires.Dresses",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
662 "X..Balanes.Vivantes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
663 #"Commentaires.Avant",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
664 "X..Surface.Accolement", # is NA, then replace by 0 as well because no sense to have a NA value for "% surface accolement" as well.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
665 #"Type.sustrat.observé",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
666 #"Commentaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
667 "Nb.Cancer.pagurus..Tourteau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
668 "Nb.Necora.puber..Etrille.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
669 "Nb.Carcinus.maenas..Crabe.vert.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
670 "Nb.Nucella.lapilus..Pourpre.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
671 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
672 #.."Nb.Octopus.vulgaris..Poulpe.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
673 "Nb.Galathea..Galathées.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
674 #.."Nb.Paracentrotus.lividus..Oursin.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
675 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
676 "Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
677 "Nb.Haliotis.tuberculata..Ormeau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
678 #"Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
679 "Nb.Littorina.littorea..Bigorneau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
680 "Nb.Xantho.pilipes..Xanthe.poilu.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
681 "Nb.Mimachlamys.varia..Pétoncle.noir."
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
682 )
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
683 ] <- lapply(bretagne_bm[, c(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
684 "X..algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
685 "Strate.algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
686 "X..algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
687 "Strate.algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
688 "X..algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
689 "Strate.algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
690 "X..Cladophora",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
691 "X..Lithophyllum",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
692 "X..Recouvrement.Sediment", # is NA, then replace by 0 as well because no sense to have a NA value for "% recouvrement sédiment" as well.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
693 #"Type.Sediment",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
694 "X..Roche.Nue", # is NA, then replace by 0 as well because no sense to have a NA value for "% roche nue" as well.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
695 "Nb.Littorina.obtusata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
696 "Nb.Gibbula.cineraria",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
697 "Nb.Gibbula.pennanti",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
698 "Nb.Gibbula.umbilicalis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
699 "Nb.Phallusia.mamillata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
700 "Nb.Tethya.aurantium",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
701 #"Nb.Spirobranchus.lamarckii.1B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
702 #"Nb.Spirobranchus.lamarckii.2B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
703 #"Nb.Spirobranchus.lamarckii.3B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
704 #"Nb.Spirobranchus.lamarckii.4B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
705 #"Nb.Spirobranchus.lamarckii.5B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
706 "Nb.Spirobranchus.lamarckii.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
707 #"Nb.spirorbis.1A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
708 #"Nb.spirorbis.2A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
709 #"Nb.spirorbis.3A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
710 #"Nb.spirorbis.4A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
711 #"Nb.spirorbis.5A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
712 "Nb.spirorbis.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
713 #.."Nb.Crassostrea.gigas",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
714 #.."Nb.Ostrea.edulis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
715 #.."X..Mytilus.sp.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
716 #.."X..Hermelles",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
717 #.."X..Hydraires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
718 "X..Eponges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
719 "X..Ascidies.Coloniales",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
720 "X..Ascidies.Solitaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
721 "X..Bryozoaires.Dresses",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
722 "X..Balanes.Vivantes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
723 #"Commentaires.Avant",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
724 "X..Surface.Accolement", # is NA, then replace by 0 as well because no sense to have a NA value for "% surface accolement" as well.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
725 #"Type.sustrat.observé",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
726 #"Commentaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
727 "Nb.Cancer.pagurus..Tourteau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
728 "Nb.Necora.puber..Etrille.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
729 "Nb.Carcinus.maenas..Crabe.vert.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
730 "Nb.Nucella.lapilus..Pourpre.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
731 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
732 #.."Nb.Octopus.vulgaris..Poulpe.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
733 "Nb.Galathea..Galathées.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
734 #.."Nb.Paracentrotus.lividus..Oursin.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
735 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
736 "Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
737 "Nb.Haliotis.tuberculata..Ormeau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
738 #"Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
739 "Nb.Littorina.littorea..Bigorneau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
740 "Nb.Xantho.pilipes..Xanthe.poilu.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
741 "Nb.Mimachlamys.varia..Pétoncle.noir."
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
742 )
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
743 ], function(x) replace(x, is.na(x), 0))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
744
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
745
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
746 # bretagne_bf
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
747 bretagne_bf[, c(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
748 "X..algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
749 "Strate.algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
750 "X..algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
751 "Strate.algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
752 "X..algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
753 "Strate.algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
754 "X..Cladophora",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
755 "X..Lithophyllum",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
756 "X..Recouvrement.Sediment", # is NA, then replace by 0 as well because no sense to have a NA value for "% recouvrement sédiment" as well.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
757 #"Type.Sediment",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
758 "X..Roche.Nue", # is NA, then replace by 0 as well because no sense to have a NA value for "% roche nue" as well.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
759 "Nb.Littorina.obtusata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
760 "Nb.Gibbula.cineraria",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
761 "Nb.Gibbula.pennanti",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
762 "Nb.Gibbula.umbilicalis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
763 "Nb.Phallusia.mamillata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
764 "Nb.Tethya.aurantium",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
765 #"Nb.Spirobranchus.lamarckii.1B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
766 #"Nb.Spirobranchus.lamarckii.2B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
767 #"Nb.Spirobranchus.lamarckii.3B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
768 #"Nb.Spirobranchus.lamarckii.4B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
769 #"Nb.Spirobranchus.lamarckii.5B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
770 "Nb.Spirobranchus.lamarckii.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
771 #"Nb.spirorbis.1A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
772 #"Nb.spirorbis.2A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
773 #"Nb.spirorbis.3A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
774 #"Nb.spirorbis.4A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
775 #"Nb.spirorbis.5A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
776 "Nb.spirorbis.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
777 #.."Nb.Crassostrea.gigas",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
778 #.."Nb.Ostrea.edulis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
779 #.."X..Mytilus.sp.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
780 #.."X..Hermelles",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
781 #.."X..Hydraires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
782 "X..Eponges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
783 "X..Ascidies.Coloniales",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
784 "X..Ascidies.Solitaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
785 "X..Bryozoaires.Dresses",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
786 "X..Balanes.Vivantes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
787 #"Commentaires.Avant",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
788 "X..Surface.Accolement"#, # is NA, then replace by 0 as well because no sense to have a NA value for "% surface accolement" as well.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
789 #"Type.sustrat.observé",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
790 #"Commentaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
791 #."Nb.Cancer.pagurus..Tourteau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
792 #.."Nb.Necora.puber..Etrille.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
793 #."Nb.Carcinus.maenas..Crabe.vert.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
794 #."Nb.Nucella.lapilus..Pourpre.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
795 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
796 #.."Nb.Octopus.vulgaris..Poulpe.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
797 #."Nb.Galathea..Galathées.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
798 #.."Nb.Paracentrotus.lividus..Oursin.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
799 #."Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
800 #."Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
801 #."Nb.Haliotis.tuberculata..Ormeau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
802 #."Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
803 #."Nb.Littorina.littorea..Bigorneau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
804 #."Nb.Xantho.pilipes..Xanthe.poilu.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
805 #."Nb.Mimachlamys.varia..Pétoncle.noir."
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
806 )
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
807 ] <- lapply(bretagne_bf[, c(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
808 "X..algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
809 "Strate.algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
810 "X..algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
811 "Strate.algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
812 "X..algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
813 "Strate.algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
814 "X..Cladophora",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
815 "X..Lithophyllum",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
816 "X..Recouvrement.Sediment", # is NA, then replace by 0 as well because no sense to have a NA value for "% recouvrement sédiment" as well.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
817 #"Type.Sediment",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
818 "X..Roche.Nue", # is NA, then replace by 0 as well because no sense to have a NA value for "% roche nue" as well.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
819 "Nb.Littorina.obtusata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
820 "Nb.Gibbula.cineraria",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
821 "Nb.Gibbula.pennanti",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
822 "Nb.Gibbula.umbilicalis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
823 "Nb.Phallusia.mamillata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
824 "Nb.Tethya.aurantium",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
825 #"Nb.Spirobranchus.lamarckii.1B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
826 #"Nb.Spirobranchus.lamarckii.2B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
827 #"Nb.Spirobranchus.lamarckii.3B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
828 #"Nb.Spirobranchus.lamarckii.4B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
829 #"Nb.Spirobranchus.lamarckii.5B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
830 "Nb.Spirobranchus.lamarckii.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
831 #"Nb.spirorbis.1A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
832 #"Nb.spirorbis.2A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
833 #"Nb.spirorbis.3A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
834 #"Nb.spirorbis.4A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
835 #"Nb.spirorbis.5A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
836 "Nb.spirorbis.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
837 #.."Nb.Crassostrea.gigas",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
838 #.."Nb.Ostrea.edulis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
839 #.."X..Mytilus.sp.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
840 #.."X..Hermelles",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
841 #.."X..Hydraires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
842 "X..Eponges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
843 "X..Ascidies.Coloniales",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
844 "X..Ascidies.Solitaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
845 "X..Bryozoaires.Dresses",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
846 "X..Balanes.Vivantes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
847 #"Commentaires.Avant",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
848 "X..Surface.Accolement"#, # is NA, then replace by 0 as well because no sense to have a NA value for "% surface accolement" as well.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
849 #"Type.sustrat.observé",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
850 #"Commentaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
851 #."Nb.Cancer.pagurus..Tourteau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
852 #.."Nb.Necora.puber..Etrille.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
853 #."Nb.Carcinus.maenas..Crabe.vert.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
854 #."Nb.Nucella.lapilus..Pourpre.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
855 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
856 #.."Nb.Octopus.vulgaris..Poulpe.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
857 #."Nb.Galathea..Galathées.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
858 #.."Nb.Paracentrotus.lividus..Oursin.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
859 #."Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
860 #."Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
861 #."Nb.Haliotis.tuberculata..Ormeau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
862 #."Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
863 #."Nb.Littorina.littorea..Bigorneau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
864 #."Nb.Xantho.pilipes..Xanthe.poilu.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
865 #."Nb.Mimachlamys.varia..Pétoncle.noir."
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
866 )
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
867 ], function(x) replace(x, is.na(x), 0))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
868
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
869
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
870 # egmp_basq_bm
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
871 egmp_basq_bm[, c(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
872 "X..algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
873 "Strate.algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
874 "X..algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
875 "Strate.algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
876 "X..algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
877 "Strate.algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
878 "X..Cladophora",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
879 "X..Lithophyllum",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
880 "X..Recouvrement.Sediment", # is NA, then replace by 0 as well because no sense to have a NA value for "% recouvrement sédiment" as well.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
881 #"Type.Sediment",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
882 "X..Roche.Nue", # is NA, then replace by 0 as well because no sense to have a NA value for "% roche nue" as well.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
883 "Nb.Littorina.obtusata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
884 "Nb.Gibbula.cineraria",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
885 "Nb.Gibbula.pennanti",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
886 "Nb.Gibbula.umbilicalis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
887 "Nb.Phallusia.mamillata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
888 "Nb.Tethya.aurantium",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
889 #"Nb.Spirobranchus.lamarckii.1B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
890 #"Nb.Spirobranchus.lamarckii.2B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
891 #"Nb.Spirobranchus.lamarckii.3B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
892 #"Nb.Spirobranchus.lamarckii.4B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
893 #"Nb.Spirobranchus.lamarckii.5B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
894 "Nb.Spirobranchus.lamarckii.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
895 #"Nb.spirorbis.1A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
896 #"Nb.spirorbis.2A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
897 #"Nb.spirorbis.3A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
898 #"Nb.spirorbis.4A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
899 #"Nb.spirorbis.5A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
900 "Nb.spirorbis.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
901 "Nb.Crassostrea.gigas",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
902 "Nb.Ostrea.edulis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
903 "X..Mytilus.sp.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
904 "X..Hermelles",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
905 "X..Hydraires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
906 "X..Eponges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
907 "X..Ascidies.Coloniales",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
908 "X..Ascidies.Solitaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
909 "X..Bryozoaires.Dresses",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
910 "X..Balanes.Vivantes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
911 #"Commentaires.Avant",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
912 "X..Surface.Accolement", # is NA, then replace by 0 as well because no sense to have a NA value for "% surface accolement" as well.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
913 #"Type.sustrat.observé",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
914 #"Commentaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
915 "Nb.Cancer.pagurus..Tourteau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
916 "Nb.Necora.puber..Etrille.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
917 "Nb.Carcinus.maenas..Crabe.vert.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
918 "Nb.Nucella.lapilus..Pourpre.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
919 "Nb.Eriphia.verrucosa..Crabe.verruqueux.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
920 "Nb.Octopus.vulgaris..Poulpe.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
921 "Nb.Galathea..Galathées.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
922 "Nb.Paracentrotus.lividus..Oursin.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
923 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
924 "Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
925 "Nb.Haliotis.tuberculata..Ormeau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
926 "Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
927 "Nb.Littorina.littorea..Bigorneau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
928 "Nb.Xantho.pilipes..Xanthe.poilu.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
929 "Nb.Mimachlamys.varia..Pétoncle.noir."
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
930 )
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
931 ] <- lapply(egmp_basq_bm[, c(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
932 "X..algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
933 "Strate.algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
934 "X..algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
935 "Strate.algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
936 "X..algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
937 "Strate.algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
938 "X..Cladophora",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
939 "X..Lithophyllum",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
940 "X..Recouvrement.Sediment", # is NA, then replace by 0 as well because no sense to have a NA value for "% recouvrement sédiment" as well.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
941 #"Type.Sediment",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
942 "X..Roche.Nue", # is NA, then replace by 0 as well because no sense to have a NA value for "% roche nue" as well.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
943 "Nb.Littorina.obtusata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
944 "Nb.Gibbula.cineraria",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
945 "Nb.Gibbula.pennanti",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
946 "Nb.Gibbula.umbilicalis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
947 "Nb.Phallusia.mamillata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
948 "Nb.Tethya.aurantium",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
949 #"Nb.Spirobranchus.lamarckii.1B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
950 #"Nb.Spirobranchus.lamarckii.2B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
951 #"Nb.Spirobranchus.lamarckii.3B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
952 #"Nb.Spirobranchus.lamarckii.4B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
953 #"Nb.Spirobranchus.lamarckii.5B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
954 "Nb.Spirobranchus.lamarckii.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
955 #"Nb.spirorbis.1A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
956 #"Nb.spirorbis.2A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
957 #"Nb.spirorbis.3A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
958 #"Nb.spirorbis.4A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
959 #"Nb.spirorbis.5A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
960 "Nb.spirorbis.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
961 "Nb.Crassostrea.gigas",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
962 "Nb.Ostrea.edulis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
963 "X..Mytilus.sp.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
964 "X..Hermelles",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
965 "X..Hydraires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
966 "X..Eponges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
967 "X..Ascidies.Coloniales",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
968 "X..Ascidies.Solitaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
969 "X..Bryozoaires.Dresses",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
970 "X..Balanes.Vivantes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
971 #"Commentaires.Avant",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
972 "X..Surface.Accolement", # is NA, then replace by 0 as well because no sense to have a NA value for "% surface accolement" as well.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
973 #"Type.sustrat.observé",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
974 #"Commentaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
975 "Nb.Cancer.pagurus..Tourteau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
976 "Nb.Necora.puber..Etrille.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
977 "Nb.Carcinus.maenas..Crabe.vert.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
978 "Nb.Nucella.lapilus..Pourpre.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
979 "Nb.Eriphia.verrucosa..Crabe.verruqueux.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
980 "Nb.Octopus.vulgaris..Poulpe.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
981 "Nb.Galathea..Galathées.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
982 "Nb.Paracentrotus.lividus..Oursin.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
983 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
984 "Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
985 "Nb.Haliotis.tuberculata..Ormeau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
986 "Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
987 "Nb.Littorina.littorea..Bigorneau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
988 "Nb.Xantho.pilipes..Xanthe.poilu.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
989 "Nb.Mimachlamys.varia..Pétoncle.noir."
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
990 )
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
991 ], function(x) replace(x, is.na(x), 0))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
992
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
993
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
994 # egmp_basq_bf
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
995 egmp_basq_bf[, c(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
996 "X..algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
997 "Strate.algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
998 "X..algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
999 "Strate.algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1000 "X..algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1001 "Strate.algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1002 "X..Cladophora",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1003 "X..Lithophyllum",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1004 "X..Recouvrement.Sediment", # is NA, then replace by 0 as well because no sense to have a NA value for "% recouvrement sédiment" as well.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1005 #"Type.Sediment",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1006 "X..Roche.Nue", # is NA, then replace by 0 as well because no sense to have a NA value for "% roche nue" as well.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1007 "Nb.Littorina.obtusata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1008 "Nb.Gibbula.cineraria",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1009 "Nb.Gibbula.pennanti",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1010 "Nb.Gibbula.umbilicalis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1011 "Nb.Phallusia.mamillata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1012 "Nb.Tethya.aurantium",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1013 #"Nb.Spirobranchus.lamarckii.1B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1014 #"Nb.Spirobranchus.lamarckii.2B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1015 #"Nb.Spirobranchus.lamarckii.3B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1016 #"Nb.Spirobranchus.lamarckii.4B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1017 #"Nb.Spirobranchus.lamarckii.5B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1018 "Nb.Spirobranchus.lamarckii.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1019 #"Nb.spirorbis.1A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1020 #"Nb.spirorbis.2A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1021 #"Nb.spirorbis.3A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1022 #"Nb.spirorbis.4A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1023 #"Nb.spirorbis.5A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1024 "Nb.spirorbis.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1025 "Nb.Crassostrea.gigas",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1026 "Nb.Ostrea.edulis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1027 "X..Mytilus.sp.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1028 "X..Hermelles",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1029 "X..Hydraires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1030 "X..Eponges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1031 "X..Ascidies.Coloniales",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1032 "X..Ascidies.Solitaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1033 "X..Bryozoaires.Dresses",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1034 "X..Balanes.Vivantes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1035 #"Commentaires.Avant",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1036 "X..Surface.Accolement"#, # is NA, then replace by 0 as well because no sense to have a NA value for "% surface accolement" as well.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1037 #"Type.sustrat.observé",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1038 #"Commentaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1039 #."Nb.Cancer.pagurus..Tourteau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1040 #.."Nb.Necora.puber..Etrille.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1041 #."Nb.Carcinus.maenas..Crabe.vert.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1042 #."Nb.Nucella.lapilus..Pourpre.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1043 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1044 #.."Nb.Octopus.vulgaris..Poulpe.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1045 #."Nb.Galathea..Galathées.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1046 #.."Nb.Paracentrotus.lividus..Oursin.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1047 #."Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1048 #."Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1049 #."Nb.Haliotis.tuberculata..Ormeau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1050 #."Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1051 #."Nb.Littorina.littorea..Bigorneau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1052 #."Nb.Xantho.pilipes..Xanthe.poilu.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1053 #."Nb.Mimachlamys.varia..Pétoncle.noir."
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1054 )
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1055 ] <- lapply(egmp_basq_bf[, c(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1056 "X..algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1057 "Strate.algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1058 "X..algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1059 "Strate.algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1060 "X..algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1061 "Strate.algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1062 "X..Cladophora",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1063 "X..Lithophyllum",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1064 "X..Recouvrement.Sediment", # is NA, then replace by 0 as well because no sense to have a NA value for "% recouvrement sédiment" as well.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1065 #"Type.Sediment",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1066 "X..Roche.Nue", # is NA, then replace by 0 as well because no sense to have a NA value for "% roche nue" as well.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1067 "Nb.Littorina.obtusata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1068 "Nb.Gibbula.cineraria",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1069 "Nb.Gibbula.pennanti",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1070 "Nb.Gibbula.umbilicalis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1071 "Nb.Phallusia.mamillata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1072 "Nb.Tethya.aurantium",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1073 #"Nb.Spirobranchus.lamarckii.1B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1074 #"Nb.Spirobranchus.lamarckii.2B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1075 #"Nb.Spirobranchus.lamarckii.3B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1076 #"Nb.Spirobranchus.lamarckii.4B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1077 #"Nb.Spirobranchus.lamarckii.5B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1078 "Nb.Spirobranchus.lamarckii.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1079 #"Nb.spirorbis.1A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1080 #"Nb.spirorbis.2A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1081 #"Nb.spirorbis.3A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1082 #"Nb.spirorbis.4A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1083 #"Nb.spirorbis.5A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1084 "Nb.spirorbis.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1085 "Nb.Crassostrea.gigas",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1086 "Nb.Ostrea.edulis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1087 "X..Mytilus.sp.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1088 "X..Hermelles",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1089 "X..Hydraires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1090 "X..Eponges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1091 "X..Ascidies.Coloniales",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1092 "X..Ascidies.Solitaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1093 "X..Bryozoaires.Dresses",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1094 "X..Balanes.Vivantes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1095 #"Commentaires.Avant",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1096 "X..Surface.Accolement"#, # is NA, then replace by 0 as well because no sense to have a NA value for "% surface accolement" as well.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1097 #"Type.sustrat.observé",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1098 #"Commentaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1099 #."Nb.Cancer.pagurus..Tourteau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1100 #.."Nb.Necora.puber..Etrille.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1101 #."Nb.Carcinus.maenas..Crabe.vert.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1102 #."Nb.Nucella.lapilus..Pourpre.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1103 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1104 #.."Nb.Octopus.vulgaris..Poulpe.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1105 #."Nb.Galathea..Galathées.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1106 #.."Nb.Paracentrotus.lividus..Oursin.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1107 #."Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1108 #."Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1109 #."Nb.Haliotis.tuberculata..Ormeau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1110 #."Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1111 #."Nb.Littorina.littorea..Bigorneau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1112 #."Nb.Xantho.pilipes..Xanthe.poilu.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1113 #."Nb.Mimachlamys.varia..Pétoncle.noir."
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1114 )
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1115 ], function(x) replace(x, is.na(x), 0))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1116
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1117
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1118 # merge dfs.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1119 qecbnato0 <- dplyr::bind_rows(bretagne_bm, bretagne_bf)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1120 qecbnato0 <- dplyr::bind_rows(qecbnato0, egmp_basq_bm)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1121 qecbnato0 <- dplyr::bind_rows(qecbnato0, egmp_basq_bf)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1122
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1123 qecbnato0 <- dplyr::arrange(qecbnato0, region, site_year_month_day, Type.Bloc, Numéro.Bloc.échantillon, Face)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1124
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1125 rm(bretagne_bm, bretagne_bf, egmp_basq_bm, egmp_basq_bf)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1126
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1127
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1128 ## analyse matricielle
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1129
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1130 # NB some variables were dplyr::renamed or created, cfr I originally merged qecb and ivr data in below script to do some correlation analysis. This is not the case anymore, so no more merging anymore.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1131
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1132 qecbnato0 <- tibble::add_column(qecbnato0, region.site_year_month_day = paste0(qecbnato0$region, qecbnato0$site_year_month_day), .before = "region")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1133
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1134
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1135 numero_quadrat <- stringr::str_sub(qecbnato0$quadrat_bis, start = -1)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1136 qecbnato0 <- tibble::add_column(qecbnato0, numero_quadrat, .after = "quadrat_bis")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1137 rm(numero_quadrat)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1138 qecbnato0$numero_quadrat <- as.integer(qecbnato0$numero_quadrat)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1139
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1140
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1141 qecbnato0$Year <- as.integer(qecbnato0$Year)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1142 qecbnato0$Month <- as.integer(qecbnato0$Month)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1143 qecbnato0$Day <- as.integer(qecbnato0$Day)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1144
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1145 ############################################################
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1146 #!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1147 # Anna still hasn't corrected for boulder nb in FINS_Quemenes.2020.10.16 data encoding ! removed from the df_
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1148 qecbnato0 <- qecbnato0 %>% dplyr::filter(site_year_month_day != "FINS_Quemenes.2020.10.16")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1149 ############################################################
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1150
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1151 # what to do with spirorbes & Nb.Spirobranchus.lamarckii.total? log10 transformation
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1152
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1153 qecbnato0 <- tibble::add_column(qecbnato0, log10.Nb.spirorbis.total = log10(qecbnato0$Nb.spirorbis.total + 1), .after = "Nb.spirorbis.total")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1154 qecbnato0 <- tibble::add_column(qecbnato0, log10.Nb.Spirobranchus.lamarckii.total = log10(qecbnato0$Nb.Spirobranchus.lamarckii.total + 1), .after = "Nb.Spirobranchus.lamarckii.total")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1155
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1156 saveRDS(qecbnato0, "qecbnato0.RDS")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1157
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1158
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1159 ###############################################################
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1160 # #
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1161 # Start dissimilarity calculation with some data handling #
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1162 # #
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1163 ###############################################################
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1164
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1165 # first, create vector (4) for qecb and fishing by region (same as above)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1166
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1167 bret_egmp_basq_qecb <- c(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1168 "X..algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1169 "X..algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1170 "X..algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1171 "X..Cladophora",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1172 "X..Lithophyllum",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1173 "Nb.Littorina.obtusata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1174 "Nb.Gibbula.cineraria",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1175 "Nb.Gibbula.pennanti",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1176 "Nb.Gibbula.umbilicalis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1177 "Nb.Phallusia.mamillata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1178 "Nb.Tethya.aurantium",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1179 "Nb.Spirobranchus.lamarckii.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1180 "Nb.spirorbis.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1181 "X..Eponges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1182 "X..Ascidies.Coloniales",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1183 "X..Ascidies.Solitaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1184 "X..Bryozoaires.Dresses",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1185 "X..Balanes.Vivantes"
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1186 #, "X..Recouvrement.Sediment"
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1187 #, "X..Roche.Nue"
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1188 #, "X..Surface.Accolement"
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1189 )
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1190
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1191 egmp_basq_qecb <- c("Nb.Crassostrea.gigas", "Nb.Ostrea.edulis", "X..Mytilus.sp.", "X..Hermelles", "X..Hydraires")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1192
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1193 bret_egmp_basq_fishing <- c("Nb.Cancer.pagurus..Tourteau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1194 "Nb.Necora.puber..Etrille.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1195 "Nb.Carcinus.maenas..Crabe.vert.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1196 "Nb.Nucella.lapilus..Pourpre.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1197 "Nb.Galathea..Galathées.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1198 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1199 "Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1200 "Nb.Haliotis.tuberculata..Ormeau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1201 "Nb.Littorina.littorea..Bigorneau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1202 "Nb.Xantho.pilipes..Xanthe.poilu.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1203 "Nb.Mimachlamys.varia..Pétoncle.noir.")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1204
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1205 egmp_basq_fishing <- c("Nb.Eriphia.verrucosa..Crabe.verruqueux.", "Nb.Octopus.vulgaris..Poulpe.", "Nb.Paracentrotus.lividus..Oursin.", "Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1206
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1207 # here I can choose to either replace spirorbis and/or spirobranchus by their log10 transformation in bret_egmp_basq_qecb vector
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1208 bret_egmp_basq_qecb <- replace(bret_egmp_basq_qecb, bret_egmp_basq_qecb == "Nb.spirorbis.total", "log10.Nb.spirorbis.total")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1209 saveRDS(bret_egmp_basq_qecb, "bret_egmp_basq_qecb.RDS")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1210
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1211
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1212 #############################################################
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1213 # #
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1214 # Compute dissimilarity #
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1215 # #
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1216 #############################################################
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1217 ### determination of coefficient of dissimilarity face sup mobile bloc vs fixed bloc
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1218
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1219 # loop in a fct
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1220
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1221 matri_fct_bmf <- function(data, conca) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1222
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1223 matri_df <- data
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1224
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1225 for (x in c(1:length(unique(matri_df$site_year_month_day)))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1226
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1227 qecbnato0_x <- matri_df %>% dplyr::filter(site_year_month_day == unique(matri_df$site_year_month_day)[[x]])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1228
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1229 rownames(qecbnato0_x) <- paste0(qecbnato0_x$Type.Bloc, "_", qecbnato0_x$Face, "_", qecbnato0_x$Numéro.Bloc.échantillon, "_", qecbnato0_x$quadrat_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1230
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1231
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1232 mtxdis <- vegan::vegdist(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1233 sqrt(qecbnato0_x[, conca]), #Transform your species abundance data_ Typically, raw abundances are transformed prior to analysis. Usually you will use square root, fourth-root, log(X+1), or presence-absence (square root being least extreme, P/A being most). I would start with square root. (https://stats.stackexchange.com/questions/234495/double-zeroes-problem-with-euclidean-distance-and-abundance-data-is-the-proble)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1234
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1235 na.rm = TRUE,
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1236 method = "bray" #Construct species abundance dissimilarity matrices with Bray-Curtis. If your data contains samples that are all-zero you will run into the double zero problem. This can be overcome by using a zero-adjusted Bray-Curtis coefficient, which is sometimes referred to as a 'dummy variable' which damps down the similarity fluctuations between samples that are both zero (undefined). => see below for zero-adjusted Bray-Curtis coefficient ; #another possibility, sqrt + 1 ??
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1237 )
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1238
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1239
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1240 #https://rdrr.io/github/phytomosaic/ecole/man/bray0.html
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1241 # mtxdis <- ecole::bray0(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1242 # sqrt
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1243 # (qecbnato0_x[,conca]), na.rm = TRUE)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1244
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1245 expand.grid(mtxdis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1246
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1247 mtxdisdf_ <- as.data.frame(as.matrix(mtxdis))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1248
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1249 a_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1250 b_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1251 c_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1252 d_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1253 e_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1254 f_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1255 g_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1256 h_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1257 i_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1258 j_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1259 k_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1260 l_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1261 m_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1262 n_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1263
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1264 for (z in c(1:nrow(mtxdisdf_))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1265
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1266 a_[[z]] <- (paste0(rownames(mtxdisdf_[z + 1, ]), " & ", ifelse(nrow(mtxdisdf_) >= 1, colnames(mtxdisdf_[1]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1267 b_[[z]] <- (paste0(rownames(mtxdisdf_[z + 2, ]), " & ", ifelse(nrow(mtxdisdf_) >= 2, colnames(mtxdisdf_[2]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1268 c_[[z]] <- (paste0(rownames(mtxdisdf_[z + 3, ]), " & ", ifelse(nrow(mtxdisdf_) >= 3, colnames(mtxdisdf_[3]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1269 d_[[z]] <- (paste0(rownames(mtxdisdf_[z + 4, ]), " & ", ifelse(nrow(mtxdisdf_) >= 4, colnames(mtxdisdf_[4]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1270 e_[[z]] <- (paste0(rownames(mtxdisdf_[z + 5, ]), " & ", ifelse(nrow(mtxdisdf_) >= 5, colnames(mtxdisdf_[5]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1271 f_[[z]] <- (paste0(rownames(mtxdisdf_[z + 6, ]), " & ", ifelse(nrow(mtxdisdf_) >= 6, colnames(mtxdisdf_[6]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1272 g_[[z]] <- (paste0(rownames(mtxdisdf_[z + 7, ]), " & ", ifelse(nrow(mtxdisdf_) >= 7, colnames(mtxdisdf_[7]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1273 h_[[z]] <- (paste0(rownames(mtxdisdf_[z + 8, ]), " & ", ifelse(nrow(mtxdisdf_) >= 8, colnames(mtxdisdf_[8]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1274 i_[[z]] <- (paste0(rownames(mtxdisdf_[z + 9, ]), " & ", ifelse(nrow(mtxdisdf_) >= 9, colnames(mtxdisdf_[9]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1275 j_[[z]] <- (paste0(rownames(mtxdisdf_[z + 10, ]), " & ", ifelse(nrow(mtxdisdf_) >= 10, colnames(mtxdisdf_[10]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1276 k_[[z]] <- (paste0(rownames(mtxdisdf_[z + 11, ]), " & ", ifelse(nrow(mtxdisdf_) >= 11, colnames(mtxdisdf_[11]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1277 l_[[z]] <- (paste0(rownames(mtxdisdf_[z + 12, ]), " & ", ifelse(nrow(mtxdisdf_) >= 12, colnames(mtxdisdf_[12]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1278 m_[[z]] <- (paste0(rownames(mtxdisdf_[z + 13, ]), " & ", ifelse(nrow(mtxdisdf_) >= 13, colnames(mtxdisdf_[13]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1279 n_[[z]] <- (paste0(rownames(mtxdisdf_[z + 14, ]), " & ", ifelse(nrow(mtxdisdf_) >= 14, colnames(mtxdisdf_[14]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1280
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1281 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1282
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1283 rm(z)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1284
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1285 y <- length(a_) - (ifelse(nrow(mtxdisdf_) >= 1, 1, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1286 a_ <- a_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1287 y <- length(b_) - (ifelse(nrow(mtxdisdf_) >= 2, 2, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1288 b_ <- b_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1289 y <- length(c_) - (ifelse(nrow(mtxdisdf_) >= 3, 3, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1290 c_ <- c_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1291 y <- length(d_) - (ifelse(nrow(mtxdisdf_) >= 4, 4, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1292 d_ <- d_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1293 y <- length(e_) - (ifelse(nrow(mtxdisdf_) >= 5, 5, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1294 e_ <- e_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1295 y <- length(f_) - (ifelse(nrow(mtxdisdf_) >= 6, 6, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1296 f_ <- f_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1297 y <- length(g_) - (ifelse(nrow(mtxdisdf_) >= 7, 7, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1298 g_ <- g_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1299 y <- length(h_) - (ifelse(nrow(mtxdisdf_) >= 8, 8, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1300 h_ <- h_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1301 y <- length(i_) - (ifelse(nrow(mtxdisdf_) >= 9, 9, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1302 i_ <- i_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1303 y <- length(j_) - (ifelse(nrow(mtxdisdf_) >= 10, 10, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1304 j_ <- j_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1305 y <- length(k_) - (ifelse(nrow(mtxdisdf_) >= 11, 11, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1306 k_ <- k_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1307 y <- length(l_) - (ifelse(nrow(mtxdisdf_) >= 12, 12, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1308 l_ <- l_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1309 y <- length(m_) - (ifelse(nrow(mtxdisdf_) >= 13, 13, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1310 m_ <- m_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1311 y <- length(n_) - (ifelse(nrow(mtxdisdf_) >= 14, 14, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1312 n_ <- n_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1313
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1314 rm(y)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1315
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1316 name_ <- c(a_, b_, c_, d_, e_, f_, g_, h_, i_, j_, k_, l_, m_, n_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1317 df_ <- data.frame(expand.grid(mtxdis), name_[1:nrow(expand.grid(mtxdis))])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1318 names(df_) <- c("dist.", "name_")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1319
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1320 rm(a_, b_, c_, d_, e_, f_, g_, h_, i_, j_, k_, l_, m_, n_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1321 rm(name_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1322
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1323 q_ <- strsplit(df_$name_, " & ")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1324 mat_ <- matrix(unlist(q_), ncol = 2, byrow = TRUE)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1325 q_df_ <- as.data.frame(matrix(unlist(q_), ncol = 2, byrow = TRUE))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1326 df_ <- dplyr::bind_cols(df_, q_df_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1327
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1328 rm(q_, mat_, q_df_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1329
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1330 split_ <- strsplit(df_$V1, "_")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1331 v1_split_ <- as.data.frame(matrix(unlist(split_), ncol = 4, byrow = TRUE))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1332 split_ <- strsplit(df_$V2, "_")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1333 v2_split_ <- as.data.frame(matrix(unlist(split_), ncol = 4, byrow = TRUE))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1334
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1335 df_ <- dplyr::bind_cols(df_, v1_split_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1336 df_ <- dplyr::bind_cols(df_, v2_split_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1337 df_red_ <- subset(df_, V4...8 == V4...12 & V1...5 != V1...9)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1338 site_year_month_day <- rep(unique(qecbnato0_x$site_year_month_day), nrow(df_red_))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1339
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1340 df_red_ <- tibble::add_column(df_red_, site_year_month_day, .before = "dist.")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1341
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1342 rm(split_, v1_split_, v2_split_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1343 rm(mtxdis, mtxdisdf_, df_, site_year_month_day)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1344
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1345 matri_list[[x]] <- df_red_
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1346 matri_list <<- matri_list
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1347
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1348 rm(df_red_, qecbnato0_x, x)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1349
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1350 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1351
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1352 matri_df <- do.call("rbind", matri_list)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1353
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1354 names(matri_df) <- c("site_year_month_day", "dist.", "name_", "name_left", "name_right", "Type.Bloc.left", "Face.left", "Numéro.Bloc.échantillon.left", "Quadrat.left", "Type.Bloc.right", "Face.right", "Numéro.Bloc.échantillon.right", "Quadrat.right")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1355
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1356 matri_df <<- matri_df
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1357
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1358 hist(matri_df$dist.)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1359
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1360 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1361
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1362 data_ <- dplyr::filter(qecbnato0, Face == "face supérieure")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1363 data_$Type.Bloc <- ifelse(as.character(data_$Type.Bloc) == "Roche en place", "Bloc fixé", as.character(data_$Type.Bloc))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1364 matri_list <- vector("list", length(unique(data_$site_year_month_day)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1365
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1366 matri_fct_bmf(data = data_, conca = c(bret_egmp_basq_qecb, egmp_basq_qecb))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1367 hist(matri_df$dist., main = c(paste("Histo. of Bray (0-adjusted) dist. dissimilarity measures"), paste(" (sqrt transfo) - BMfs vs BF -")))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1368
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1369 matri_full_bm_bf_fs <- matri_df
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1370
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1371
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1372 rm(data_, matri_df, matri_list)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1373
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1374
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1375 ### determination of coefficient of dissimilarity between blocs mobiles face sup vs face inf.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1376
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1377 # loop in a fct
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1378
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1379 matri_fct_bmm <- function(data, conca) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1380
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1381 matri_df <- data
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1382
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1383 for (x in c(1:length(unique(matri_df$site_year_month_day)))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1384
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1385 qecbnato0_x <- matri_df %>% dplyr::filter(site_year_month_day == unique(matri_df$site_year_month_day)[[x]])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1386
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1387 rownames(qecbnato0_x) <- paste0(qecbnato0_x$Type.Bloc, "_", qecbnato0_x$Face, "_", qecbnato0_x$Numéro.Bloc.échantillon, "_", qecbnato0_x$quadrat_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1388
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1389
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1390 mtxdis <- vegan::vegdist(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1391 sqrt(qecbnato0_x[, c(bret_egmp_basq_qecb)]), #Transform your species abundance data_ Typically, raw abundances are transformed prior to analysis. Usually you will use square root, fourth-root, log(X+1), or presence-absence (square root being least extreme, P/A being most). I would start with square root. (https://stats.stackexchange.com/questions/234495/double-zeroes-problem-with-euclidean-distance-and-abundance-data-is-the-proble)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1392 na.rm = TRUE,
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1393 method = "bray" #Construct species abundance dissimilarity matrices with Bray-Curtis. If your data contains samples that are all-zero you will run into the double zero problem. This can be overcome by using a zero-adjusted Bray-Curtis coefficient, which is sometimes referred to as a 'dummy variable' which damps down the similarity fluctuations between samples that are both zero (undefined). => see below for zero-adjusted Bray-Curtis coefficient ; #another possibility, sqrt + 1 ??
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1394 )
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1395
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1396
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1397 #mtxdis <- ecole::bray0(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1398 # sqrt(qecbnato0_x[, conca]), na.rm = TRUE)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1399
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1400
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1401 expand.grid(mtxdis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1402
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1403 mtxdisdf_ <- as.data.frame(as.matrix(mtxdis))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1404
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1405 a_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1406 b_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1407 c_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1408 d_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1409 e_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1410 f_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1411 g_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1412 h_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1413 i_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1414 j_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1415 k_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1416 l_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1417 m_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1418 n_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1419 o_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1420 p_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1421 q_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1422 r_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1423 s_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1424
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1425 for (z in c(1:nrow(mtxdisdf_))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1426
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1427 a_[[z]] <- (paste0(rownames(mtxdisdf_[z + 1, ]), " & ", ifelse(nrow(mtxdisdf_) >= 1, colnames(mtxdisdf_[1]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1428 b_[[z]] <- (paste0(rownames(mtxdisdf_[z + 2, ]), " & ", ifelse(nrow(mtxdisdf_) >= 2, colnames(mtxdisdf_[2]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1429 c_[[z]] <- (paste0(rownames(mtxdisdf_[z + 3, ]), " & ", ifelse(nrow(mtxdisdf_) >= 3, colnames(mtxdisdf_[3]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1430 d_[[z]] <- (paste0(rownames(mtxdisdf_[z + 4, ]), " & ", ifelse(nrow(mtxdisdf_) >= 4, colnames(mtxdisdf_[4]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1431 e_[[z]] <- (paste0(rownames(mtxdisdf_[z + 5, ]), " & ", ifelse(nrow(mtxdisdf_) >= 5, colnames(mtxdisdf_[5]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1432 f_[[z]] <- (paste0(rownames(mtxdisdf_[z + 6, ]), " & ", ifelse(nrow(mtxdisdf_) >= 6, colnames(mtxdisdf_[6]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1433 g_[[z]] <- (paste0(rownames(mtxdisdf_[z + 7, ]), " & ", ifelse(nrow(mtxdisdf_) >= 7, colnames(mtxdisdf_[7]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1434 h_[[z]] <- (paste0(rownames(mtxdisdf_[z + 8, ]), " & ", ifelse(nrow(mtxdisdf_) >= 8, colnames(mtxdisdf_[8]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1435 i_[[z]] <- (paste0(rownames(mtxdisdf_[z + 9, ]), " & ", ifelse(nrow(mtxdisdf_) >= 9, colnames(mtxdisdf_[9]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1436 j_[[z]] <- (paste0(rownames(mtxdisdf_[z + 10, ]), " & ", ifelse(nrow(mtxdisdf_) >= 10, colnames(mtxdisdf_[10]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1437 k_[[z]] <- (paste0(rownames(mtxdisdf_[z + 11, ]), " & ", ifelse(nrow(mtxdisdf_) >= 11, colnames(mtxdisdf_[11]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1438 l_[[z]] <- (paste0(rownames(mtxdisdf_[z + 12, ]), " & ", ifelse(nrow(mtxdisdf_) >= 12, colnames(mtxdisdf_[12]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1439 m_[[z]] <- (paste0(rownames(mtxdisdf_[z + 13, ]), " & ", ifelse(nrow(mtxdisdf_) >= 13, colnames(mtxdisdf_[13]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1440 n_[[z]] <- (paste0(rownames(mtxdisdf_[z + 14, ]), " & ", ifelse(nrow(mtxdisdf_) >= 14, colnames(mtxdisdf_[14]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1441 o_[[z]] <- (paste0(rownames(mtxdisdf_[z + 15, ]), " & ", ifelse(nrow(mtxdisdf_) >= 15, colnames(mtxdisdf_[15]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1442 p_[[z]] <- (paste0(rownames(mtxdisdf_[z + 16, ]), " & ", ifelse(nrow(mtxdisdf_) >= 16, colnames(mtxdisdf_[16]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1443 q_[[z]] <- (paste0(rownames(mtxdisdf_[z + 17, ]), " & ", ifelse(nrow(mtxdisdf_) >= 17, colnames(mtxdisdf_[17]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1444 r_[[z]] <- (paste0(rownames(mtxdisdf_[z + 18, ]), " & ", ifelse(nrow(mtxdisdf_) >= 18, colnames(mtxdisdf_[18]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1445 s_[[z]] <- (paste0(rownames(mtxdisdf_[z + 19, ]), " & ", ifelse(nrow(mtxdisdf_) >= 19, colnames(mtxdisdf_[19]), NA)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1446
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1447 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1448
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1449 rm(z)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1450
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1451 y <- length(a_) - (ifelse(nrow(mtxdisdf_) >= 1, 1, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1452 a_ <- a_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1453 y <- length(b_) - (ifelse(nrow(mtxdisdf_) >= 2, 2, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1454 b_ <- b_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1455 y <- length(c_) - (ifelse(nrow(mtxdisdf_) >= 3, 3, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1456 c_ <- c_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1457 y <- length(d_) - (ifelse(nrow(mtxdisdf_) >= 4, 4, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1458 d_ <- d_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1459 y <- length(e_) - (ifelse(nrow(mtxdisdf_) >= 5, 5, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1460 e_ <- e_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1461 y <- length(f_) - (ifelse(nrow(mtxdisdf_) >= 6, 6, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1462 f_ <- f_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1463 y <- length(g_) - (ifelse(nrow(mtxdisdf_) >= 7, 7, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1464 g_ <- g_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1465 y <- length(h_) - (ifelse(nrow(mtxdisdf_) >= 8, 8, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1466 h_ <- h_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1467 y <- length(i_) - (ifelse(nrow(mtxdisdf_) >= 9, 9, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1468 i_ <- i_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1469 y <- length(j_) - (ifelse(nrow(mtxdisdf_) >= 10, 10, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1470 j_ <- j_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1471 y <- length(k_) - (ifelse(nrow(mtxdisdf_) >= 11, 11, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1472 k_ <- k_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1473 y <- length(l_) - (ifelse(nrow(mtxdisdf_) >= 12, 12, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1474 l_ <- l_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1475 y <- length(m_) - (ifelse(nrow(mtxdisdf_) >= 13, 13, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1476 m_ <- m_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1477 y <- length(n_) - (ifelse(nrow(mtxdisdf_) >= 14, 14, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1478 n_ <- n_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1479 y <- length(o_) - (ifelse(nrow(mtxdisdf_) >= 15, 15, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1480 o_ <- o_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1481 y <- length(p_) - (ifelse(nrow(mtxdisdf_) >= 16, 16, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1482 p_ <- p_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1483 y <- length(q_) - (ifelse(nrow(mtxdisdf_) >= 17, 17, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1484 q_ <- q_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1485 y <- length(r_) - (ifelse(nrow(mtxdisdf_) >= 18, 18, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1486 r_ <- r_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1487 y <- length(s_) - (ifelse(nrow(mtxdisdf_) >= 19, 19, nrow(mtxdisdf_)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1488 s_ <- s_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1489
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1490 rm(y)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1491
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1492 name_ <- c(a_, b_, c_, d_, e_, f_, g_, h_, i_, j_, k_, l_, m_, n_, o_, p_, q_, r_, s_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1493 df_ <- data.frame(expand.grid(mtxdis), name_[1:seq_len(nrow(expand.grid(mtxdis)))])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1494 names(df_) <- c("dist.", "name_")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1495
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1496 rm(a_, b_, c_, d_, e_, f_, g_, h_, i_, j_, k_, l_, m_, n_, o_, p_, q_, r_, s_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1497 rm(name_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1498
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1499 q_ <- strsplit(df_$name_, " & ")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1500 mat_ <- matrix(unlist(q_), ncol = 2, byrow = TRUE)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1501 q_df_ <- as.data.frame(matrix(unlist(q_), ncol = 2, byrow = TRUE))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1502 df_ <- dplyr::bind_cols(df_, q_df_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1503
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1504 rm(q_, mat_, q_df_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1505
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1506 split_ <- strsplit(df_$V1, "_")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1507 v1_split_ <- as.data.frame(matrix(unlist(split_), ncol = 4, byrow = TRUE))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1508 split_ <- strsplit(df_$V2, "_")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1509 v2_split_ <- as.data.frame(matrix(unlist(split_), ncol = 4, byrow = TRUE))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1510
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1511 df_ <- dplyr::bind_cols(df_, v1_split_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1512 df_ <- dplyr::bind_cols(df_, v2_split_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1513 df_red_ <- subset(df_, V4...8 == V4...12 & V3...7 == V3...11)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1514 site_year_month_day <- rep(unique(qecbnato0_x$site_year_month_day), nrow(df_red_))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1515
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1516 df_red_ <- tibble::add_column(df_red_, site_year_month_day, .before = "dist.")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1517
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1518 rm(split_, v1_split_, v2_split_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1519 rm(mtxdis, mtxdisdf_, df_, site_year_month_day)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1520
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1521 matri_list[[x]] <- df_red_
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1522 matri_list <<- matri_list
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1523
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1524 rm(df_red_, qecbnato0_x, x)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1525
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1526 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1527
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1528 matri_df <- do.call("rbind", matri_list)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1529
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1530 names(matri_df) <- c("site_year_month_day", "dist.", "name_", "name_left", "name_right", "Type.Bloc.left", "Face.left", "Numéro.Bloc.échantillon.left", "Quadrat.left", "Type.Bloc.right", "Face.right", "Numéro.Bloc.échantillon.right", "Quadrat.right")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1531
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1532 matri_df <<- matri_df
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1533
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1534 hist(matri_df$dist.)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1535
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1536 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1537
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1538 data_ <- dplyr::filter(qecbnato0, Type.Bloc == "Bloc mobile")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1539 matri_list <- vector("list", length(unique(data_$site_year_month_day)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1540
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1541 matri_fct_bmm(data = data_, conca = c(bret_egmp_basq_qecb, egmp_basq_qecb))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1542 hist(matri_df$dist., main = c(paste("Histo. of Bray (0-adjusted) dist. dissimilarity measures"), paste(" (sqrt transfo) - BMfs vs BMfi -")))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1543
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1544 matri_full_bm_bf_fi <- matri_df
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1545
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1546 rm(data_, matri_df, matri_list)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1547
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1548
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1549 #############################################################
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1550 # #
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1551 # Plot dissimilarity #
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1552 # #
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1553 #############################################################
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1554 ## plot
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1555
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1556 # activate line
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1557
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1558 matri_full_bm_bf_fs <- tidyr::separate(matri_full_bm_bf_fs, "site_year_month_day", into = c("departement", "Site", "Year", "Month", "Day"), remove = FALSE)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1559 matri_full_bm_bf_fs$Site <- paste0(matri_full_bm_bf_fs$departement, "_", matri_full_bm_bf_fs$Site)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1560 matri_full_bm_bf_fs <- subset(matri_full_bm_bf_fs, select = - c(departement))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1561
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1562 matri_full_bm_bf_fs <- tibble::add_column(matri_full_bm_bf_fs, Date = as.Date(paste0(matri_full_bm_bf_fs$Year, "-", matri_full_bm_bf_fs$Month, "-", matri_full_bm_bf_fs$Day), origin = "1970-01-01"), .after = "Site")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1563 matri_full_bm_bf_fs$Site <- as.factor(matri_full_bm_bf_fs$Site)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1564
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1565 matri_full_bm_bf_fi <- tidyr::separate(matri_full_bm_bf_fi, "site_year_month_day", into = c("departement", "Site", "Year", "Month", "Day"), remove = FALSE)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1566 matri_full_bm_bf_fi$Site <- paste0(matri_full_bm_bf_fi$departement, "_", matri_full_bm_bf_fi$Site)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1567 matri_full_bm_bf_fi <- subset(matri_full_bm_bf_fi, select = - c(departement))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1568 matri_full_bm_bf_fi <- tibble::add_column(matri_full_bm_bf_fi, Date = as.Date(paste0(matri_full_bm_bf_fi$Year, "-", matri_full_bm_bf_fi$Month, "-", matri_full_bm_bf_fi$Day), origin = "1970-01-01"), .after = "Site")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1569 matri_full_bm_bf_fi$Site <- as.factor(matri_full_bm_bf_fi$Site)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1570
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1571 # if error message "Error in .Call.graphics(C_palette2, .Call(C_palette2, NULL)) : invalid graphics state"
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1572
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1573
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1574 bf_fs_plot <- ggplot2::ggplot(matri_full_bm_bf_fs, ggplot2::aes(x = Site, y = dist.)) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1575 ggplot2::geom_boxplot() +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1576 #geom_jitter(shape = 16, position=position_jitter(0.2)) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1577 ggplot2::xlab("") +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1578 ggplot2::ylab("distance diss. BM.BF_FS") +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1579 ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, vjust = 0.5, hjust = 1))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1580
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1581 ggplot2::ggsave("distance_diss_BF_FS.png", bf_fs_plot, height = 4.5, width = 4)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1582
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1583 fs_fi_plot <- ggplot2::ggplot(matri_full_bm_bf_fi, ggplot2::aes(x = Site, y = dist.)) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1584 ggplot2::geom_boxplot() +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1585 #geom_jitter(shape = 16, position=position_jitter(0.2)) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1586 ggplot2::xlab("") +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1587 ggplot2::ylab("distance diss. BM_FS.FI") +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1588 ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, vjust = 0.5, hjust = 1))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1589
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1590 ggplot2::ggsave("distance_diss_FS_FI.png", fs_fi_plot, height = 4.5, width = 4)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1591
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1592 # issue with type de bloc, numéro de bloc and quadrat for df_ BM.BF_FS, cfr df_ left vs right variables doesn't give the right combination (variables with left vs right label in names come from the dissimilarity coefficient functions).
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1593 matri_full_bm_bf_fs$Quadrat <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1594 for (i in c(1:seq_len(nrow(matri_full_bm_bf_fs)))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1595 ifelse(matri_full_bm_bf_fs$Type.Bloc.left[i] == "Bloc mobile", matri_full_bm_bf_fs$Quadrat[i] <- matri_full_bm_bf_fs$Quadrat.left[i], matri_full_bm_bf_fs$Quadrat[i] <- matri_full_bm_bf_fs$Quadrat.right[i])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1596 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1597 matri_full_bm_bf_fs$Numéro.Bloc <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1598 for (i in c(1:seq_len(nrow(matri_full_bm_bf_fs)))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1599 ifelse(matri_full_bm_bf_fs$Type.Bloc.left[i] == "Bloc mobile", matri_full_bm_bf_fs$Numéro.Bloc[i] <- matri_full_bm_bf_fs$Numéro.Bloc.échantillon.left[i], matri_full_bm_bf_fs$Numéro.Bloc[i] <- matri_full_bm_bf_fs$Numéro.Bloc.échantillon.right[i])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1600 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1601
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1602 matri_full_bm_bf_fs <- tibble::add_column(matri_full_bm_bf_fs, site_year_month_day.q_BMnb = paste0(matri_full_bm_bf_fs$site_year_month_day, "_", matri_full_bm_bf_fs$Quadrat, "_", matri_full_bm_bf_fs$Numéro.Bloc), .after = "site_year_month_day")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1603 matri_full_bm_bf_fi <- tibble::add_column(matri_full_bm_bf_fi, site_year_month_day.q_BMnb = paste0(matri_full_bm_bf_fi$site_year_month_day, "_", matri_full_bm_bf_fi$Quadrat.left, "_", matri_full_bm_bf_fi$Numéro.Bloc.échantillon.left), .after = "site_year_month_day")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1604
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1605 colnames(matri_full_bm_bf_fs) <- paste("BM.BF_FS", colnames(matri_full_bm_bf_fs), sep = "_")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1606 matri_full_bm_bf_fs <- dplyr::rename(matri_full_bm_bf_fs, site_year_month_day.q_BMnb = BM.BF_FS_site_year_month_day.q_BMnb)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1607 colnames(matri_full_bm_bf_fi) <- paste("BM_FS.FI", colnames(matri_full_bm_bf_fi), sep = "_")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1608 matri_full_bm_bf_fi <- dplyr::rename(matri_full_bm_bf_fi, site_year_month_day.q_BMnb = BM_FS.FI_site_year_month_day.q_BMnb)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1609
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1610 matri_full <- dplyr::full_join(matri_full_bm_bf_fs[, c("site_year_month_day.q_BMnb", "BM.BF_FS_dist.")], matri_full_bm_bf_fi[, c("site_year_month_day.q_BMnb", "BM_FS.FI_dist.")])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1611
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1612 matri_full <- tidyr::separate(matri_full, "site_year_month_day.q_BMnb", into = c("departement", "Site", "Year", "Month", "Day", "Quadrat", "Bloc Mobile Number"), remove = FALSE)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1613 matri_full$Site <- paste0(matri_full$departement, "_", matri_full$Site)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1614 matri_full <- subset(matri_full, select = - c(departement))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1615 matri_full <- tibble::add_column(matri_full, Date = as.Date(paste0(matri_full$Year, "-", matri_full$Month, "-", matri_full$Day), origin = "1970-01-01"), .after = "Site")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1616
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1617 # Name for report/plot
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1618
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1619 matri_full <- tibble::add_column(matri_full, Site_bis = matri_full$Site, .after = "Site")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1620
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1621 matri_full$Site_bis <- ifelse(matri_full$Site == "GDMO_Locmariaquer", "Locmariaquer", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1622 matri_full$Site_bis <- ifelse(matri_full$Site == "GDMO_BegLann", "Beg Lann", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1623 matri_full$Site_bis <- ifelse(matri_full$Site == "FOUR_PlateauFour", "Plateau du Four", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1624 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_GroinCou", "Groin du Cou", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1625 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_PasEmsembert", "Le Pas d'Emsembert", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1626 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_BreeBains", "La Brée-les-Bains", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1627 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_PerreAntiochat", "Le Perré d'Antiochat", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1628 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_Chassiron", "Chassiron", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1629 matri_full$Site_bis <- ifelse(matri_full$Site == "BASQ_FlotsBleusZP", "Les Flots Bleus / zone pêcheurs", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1630 matri_full$Site_bis <- ifelse(matri_full$Site == "BASQ_FlotsBleusZF", "Les Flots Bleus / zone familles", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1631 matri_full$Site_bis <- ifelse(matri_full$Site == "GONB_IlotStMichel", "Îlot Saint-Michel", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1632 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_Quemenes", "Quéménès", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1633 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_SeinGoulenez", "Île de Sein - Goulenez", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1634 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_SeinKilaourou", "Île de Sein - Kilaourou", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1635 matri_full$Site_bis <- ifelse(matri_full$Site == "ARMO_Verdelet", "Îlot du Verdelet", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1636 matri_full$Site_bis <- ifelse(matri_full$Site == "ARMO_Piegu", "Piégu", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1637 matri_full$Site_bis <- ifelse(matri_full$Site == "ARMO_Bilfot", "Pointe de Bilfot", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1638 matri_full$Site_bis <- ifelse(matri_full$Site == "ARMO_IlePlate", "Île Plate", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1639 matri_full$Site_bis <- ifelse(matri_full$Site == "PDMO_Perharidy", "Perharidy", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1640 matri_full$Site_bis <- ifelse(matri_full$Site == "BRES_Keraliou", "Keraliou", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1641 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_Mousterlin", "Pointe de Mousterlin", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1642 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_StNicolasGlenan", "Saint-Nicolas des Glénan", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1643 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_AnseRoz", "Pointe de l'Anse du Roz", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1644
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1645 saveRDS(matri_full, "matri_full.RDS")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1646
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1647 #############################################################
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1648 # #
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1649 # Plot the dissimilarity per site #
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1650 # #
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1651 #############################################################
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1652 ## plot dissimilarity coefficient
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1653
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1654 matri_full$Year <- as.integer(matri_full$Year)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1655 matri_full$Month <- as.integer(matri_full$Month)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1656 matri_full$Day <- as.integer(matri_full$Day)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1657
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1658
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1659 ## BM_FS.FI_dist => mobile boulder upper vs lower faces
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1660
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1661 # Stats
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1662
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1663 bm_fs_fi_dist_stat <- matri_full %>% dplyr::group_by(Site, Site_bis, Date, Year, Month, Day) %>% dplyr::summarize(BM_FS.FI_dist.moy = mean(BM_FS.FI_dist., na.rm = TRUE), BM_FS.FI_dist.et = sd(BM_FS.FI_dist., na.rm = TRUE), BM_FS.FI_dist.med = median(BM_FS.FI_dist., na.rm = TRUE), BM_FS.FI_dist.min = min(BM_FS.FI_dist., na.rm = TRUE), BM_FS.FI_dist.max = max(BM_FS.FI_dist., na.rm = TRUE), nb. = dplyr::n(), nb.notNa = sum(!is.na(BM_FS.FI_dist.)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1664
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1665 bm_fs_fi_dist_stat <- dplyr::ungroup(bm_fs_fi_dist_stat)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1666
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1667 # Quality scale based on quartiles
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1668
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1669 if (choice == "N") {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1670 one <- round(mean(unlist(dplyr::filter(matri_full, BM_FS.FI_dist. <= quantile(matri_full$BM_FS.FI_dist., 0.25, na.rm = TRUE))["BM_FS.FI_dist."])), digits = 3)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1671 two <- round(mean(unlist(dplyr::filter(matri_full, BM_FS.FI_dist. > quantile(matri_full$BM_FS.FI_dist., 0.25, na.rm = TRUE) & BM_FS.FI_dist. <= quantile(matri_full$BM_FS.FI_dist., 0.5, na.rm = TRUE))["BM_FS.FI_dist."])), digits = 3)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1672 three <- round(mean(unlist(dplyr::filter(matri_full, BM_FS.FI_dist. > quantile(matri_full$BM_FS.FI_dist., 0.5, na.rm = TRUE) & BM_FS.FI_dist. <= quantile(matri_full$BM_FS.FI_dist., 0.75, na.rm = TRUE))["BM_FS.FI_dist."])), digits = 3)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1673 four <- round(mean(unlist(dplyr::filter(matri_full, BM_FS.FI_dist. > quantile(matri_full$BM_FS.FI_dist., 0.75, na.rm = TRUE))["BM_FS.FI_dist."])), digits = 3)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1674 }else {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1675 one <- 0.47
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1676 two <- 0.7
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1677 three <- 0.83
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1678 four <- 0.98
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1679 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1680
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1681 val_xmax <- as.Date(paste0(as.character(choice_date + 1), "-01-01"), origin = "1970-01-01")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1682
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1683 for (i in c(1:length(unique(bm_fs_fi_dist_stat$Site)))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1684
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1685 df1 <- dplyr::filter(bm_fs_fi_dist_stat, bm_fs_fi_dist_stat$Site == unique(bm_fs_fi_dist_stat$Site)[i])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1686
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1687 bm_fs_fi_plot <- ggplot2::ggplot() +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1688 ggplot2::geom_point(ggplot2::aes(x = bm_fs_fi_dist_stat$Date, y = bm_fs_fi_dist_stat$BM_FS.FI_dist.med), col = "grey") +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1689 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = - 0.1, ymax = one, fill = "blue"), alpha = 0.3) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1690 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = one, ymax = two, fill = "green"), alpha = 0.3) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1691 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = two, ymax = three, fill = "yellow"), alpha = 0.3) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1692 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = three, ymax = four, fill = "orange"), alpha = 0.3) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1693 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = four, ymax = 1.1, fill = "red"), alpha = 0.3) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1694 ggplot2::scale_fill_manual(values = c("#FF0000", "#F59404", "#18E125", "#1A1AE8", "#FAFA15")) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1695 ggplot2::geom_pointrange(ggplot2::aes(x = df1$Date, y = df1$BM_FS.FI_dist.med, ymin = df1$BM_FS.FI_dist.min, ymax = df1$BM_FS.FI_dist.max), col = "black") +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1696 ggplot2::xlab("Date") +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1697 ggplot2::ylab("Coef dissim BM FS-FI") +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1698 ggplot2::ggtitle(unique(df1$Site_bis)) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1699 ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, vjust = 0.5, hjust = 1), legend.position = "none")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1700
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1701 ggplot2::ggsave(paste0("fs_fi_", df1$Site, ".png"), device = "png", bm_fs_fi_plot, height = 3, width = 3.5)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1702
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1703 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1704
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1705 rm(df1, four, i, one, three, two, xmax_, xmin_, ymax_, ymin_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1706
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1707
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1708 ## BM.BF_FS_dist => mobile boulder vs fixed boulder upper faces
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1709
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1710 # Stats
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1711
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1712 bm_bf_fs_dist_stat <- matri_full %>% dplyr::group_by(Site, Site_bis, Date, Year, Month, Day) %>% dplyr::summarize(BM.BF_FS_dist.moy = mean(BM.BF_FS_dist., na.rm = TRUE), BM.BF_FS_dist.et = sd(BM.BF_FS_dist., na.rm = TRUE), BM.BF_FS_dist.med = median(BM.BF_FS_dist., na.rm = TRUE), BM.BF_FS_dist.min = min(BM.BF_FS_dist., na.rm = TRUE), BM.BF_FS_dist.max = max(BM.BF_FS_dist., na.rm = TRUE), nb. = dplyr::n(), nb.notNa = sum(!is.na(BM.BF_FS_dist.)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1713
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1714 bm_bf_fs_dist_stat <- dplyr::ungroup(bm_bf_fs_dist_stat)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1715
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1716 # Quality scale based on quartiles
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1717
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1718 if (choice == "N") {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1719 one <- round(mean(unlist(dplyr::filter(matri_full, BM.BF_FS_dist. <= quantile(matri_full$BM.BF_FS_dist., 0.25, na.rm = TRUE))["BM.BF_FS_dist."])), digits = 3)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1720 two <- round(mean(unlist(dplyr::filter(matri_full, BM.BF_FS_dist. > quantile(matri_full$BM.BF_FS_dist., 0.25, na.rm = TRUE) & BM.BF_FS_dist. <= quantile(matri_full$BM.BF_FS_dist., 0.5, na.rm = TRUE))["BM.BF_FS_dist."])), digits = 3)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1721 three <- round(mean(unlist(dplyr::filter(matri_full, BM.BF_FS_dist. > quantile(matri_full$BM.BF_FS_dist., 0.5, na.rm = TRUE) & BM.BF_FS_dist. <= quantile(matri_full$BM.BF_FS_dist., 0.75, na.rm = TRUE))["BM.BF_FS_dist."])), digits = 3)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1722 four <- round(mean(unlist(dplyr::filter(matri_full, BM.BF_FS_dist. > quantile(matri_full$BM.BF_FS_dist., 0.75, na.rm = TRUE))["BM.BF_FS_dist."])), digits = 3)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1723
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1724 }else {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1725 one <- 0.19
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1726 two <- 0.32
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1727 three <- 0.455
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1728 four <- 0.735
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1729 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1730 # Plot
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1731
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1732 for (i in c(1:length(unique(bm_bf_fs_dist_stat$Site)))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1733
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1734 df1 <- dplyr::filter(bm_bf_fs_dist_stat, bm_bf_fs_dist_stat$Site == unique(bm_bf_fs_dist_stat$Site)[i])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1735
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1736 bm_bf_fs_plot <- ggplot2::ggplot() +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1737 ggplot2::geom_point(ggplot2::aes(x = bm_bf_fs_dist_stat$Date, y = bm_bf_fs_dist_stat$BM.BF_FS_dist.med), col = "grey") +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1738 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = - 0.1, ymax = one, fill = "red"), alpha = 0.3) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1739 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = one, ymax = two, fill = "orange"), alpha = 0.3) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1740 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = two, ymax = three, fill = "yellow"), alpha = 0.3) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1741 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = three, ymax = four, fill = "green"), alpha = 0.3) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1742 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = four, ymax = 1.1, fill = "blue"), alpha = 0.3) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1743 ggplot2::scale_fill_manual(values = c("#FF0000", "#F59404", "#18E125", "#1A1AE8", "#FAFA15")) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1744 ggplot2::geom_pointrange(ggplot2::aes(x = df1$Date, y = df1$BM.BF_FS_dist.med, ymin = df1$BM.BF_FS_dist.min, ymax = df1$BM.BF_FS_dist.max), col = "black") +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1745 ggplot2::xlab("Date") +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1746 ggplot2::ylab("Coef dissim BM-BF FS") +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1747 ggplot2::ggtitle(unique(df1$Site_bis)) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1748 ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, vjust = 0.5, hjust = 1), legend.position = "none")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1749
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1750 ggplot2::ggsave(paste0("bm_bf_", df1$Site, ".png"), device = "png", bm_bf_fs_plot, height = 3, width = 3.5)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1751
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1752 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1753
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1754 rm(df1, four, i, one, three, two, xmax_, xmin_, ymax_, ymin_)