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annotate cb_dissimilarity.r @ 1:b67730406f1b draft

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planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
author ecology
date Wed, 04 Jan 2023 13:21:30 +0000
parents 8c6142630659
children bcbad4f83dec
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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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23 #####Load arguments
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25 args <- commandArgs(trailingOnly = TRUE)
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27 #####Import data
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29 if (length(args) < 1) {
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30 stop("This tool needs at least 1 argument")
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31 }else {
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32 fiche_val <- args[1]
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33 input_data <- args[2]
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34 choice <- args[3]
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35 choice_date <- as.numeric(args[4])
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36 }
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38 #############################################################
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39 # #
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40 # Loading and cleaning data #
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41 # #
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42 #############################################################
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43 # load qecb data
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45 qecb <- read.csv2(input_data, header = TRUE, fileEncoding = "Latin1") # fileEncoding = "Latin1", cfr é in variable names
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47 # import csv files ficheterrain
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49 fiche <- read.csv2(fiche_val, header = TRUE, fileEncoding = "Latin1") # fileEncoding = "Latin1", cfr é in variable names
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51 ## work on "Fiche terrain"
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53 date_fiche <- as.Date(stringr::str_sub(fiche$date.sortie, end = 10), origin = "1970-01-01")
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54 fiche <- tibble::add_column(fiche, date_fiche, .after = "date.sortie")
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55 rm(date_fiche)
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57 ## qecb vs fiche terrain
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59 fiche_red <- dplyr::filter(fiche, fiche$ID.Fiche %in% unique(qecb[, c("id")]))
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61 id_count <- qecb %>% dplyr::group_by(id) %>% dplyr::count()
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62 id_count <- dplyr::rename(id_count, "ID.Fiche" = "id")
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63 id_count <- data.frame(id_count)
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64 fiche_red <- dplyr::left_join(fiche_red, id_count)
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66 # rep fiche terrain information
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67 fiche_expanded <- fiche_red[rep(row.names(fiche_red), fiche_red$n), 1:ncol(fiche_red)]
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68 fiche_expanded <- dplyr::rename(fiche_expanded, "id" = "ID.Fiche")
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70 ## merge qecb data and ficheterrain information
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72 qecb <- dplyr::bind_cols(qecb, fiche_expanded)
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73 qecb <- dplyr::rename(qecb, "id_qecb" = "id...1")
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74 qecb <- dplyr::rename(qecb, "id_fiche" = "id...68")
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76 rm(fiche_expanded, fiche_red, id_count)
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78 qecb <- qecb %>% tidyr::separate(date_fiche, c("Year", "Month", "Day"), sep = "-", remove = FALSE)
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81 ## quadrat nb : in contrast to ivr df, quadrat number is missing for many observations in qecb df ; but from the Numero.Photo variable (boulder photo associated to field data collection), I could get back most missing quadrat numbers
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83 quadrat <- stringr::str_extract(qecb$Numero.Photo, "Q[12345]")
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84 qecb <- tibble::add_column(qecb, quadrat, .after = "Numero.Photo")
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85 rm(quadrat)
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87 # check
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88 quadrat_bis <- rep(NA, length = nrow(qecb))
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89 qecb <- tibble::add_column(qecb, quadrat_bis, .after = "quadrat")
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90 rm(quadrat_bis)
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92 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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93 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon %in% c(3, 4) & qecb$Type.Bloc == "Bloc mobile", "Q2", qecb$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(5, 6) & qecb$Type.Bloc == "Bloc mobile", "Q3", qecb$quadrat_bis)
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95 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon %in% c(7, 8) & qecb$Type.Bloc == "Bloc mobile", "Q4", qecb$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(9, 10) & qecb$Type.Bloc == "Bloc mobile", "Q5", qecb$quadrat_bis)
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99 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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100 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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101 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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102 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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103 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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104
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105 ## 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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106
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107 # Name for data analysis
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108
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109 qecb <- tibble::add_column(qecb, Site = qecb$zone.habitat, .after = "ID.Fiche")
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110
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111 for (x in seq_along(qecb$Site)) {
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112 if (grepl(pattern = "Locmariaquer", qecb$Site[x]) == TRUE) {
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113 qecb$Site[x] <- "GDMO_Locmariaquer"
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114 } else if (grepl(pattern = "Beg Lann", qecb$Site[x]) == TRUE) {
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115 qecb$Site[x] <- "GDMO_BegLann"
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116 } else if (grepl(pattern = "Plateau du Four", qecb$Site[x]) == TRUE) {
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117 qecb$Site[x] <- "FOUR_PlateauFour"
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118 } else if (grepl(pattern = "Grouin", qecb$Site[x]) == TRUE) {
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119 qecb$Site[x] <- "EGMP_GroinCou"
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120 } else if (grepl(pattern = "Ensembert", qecb$Site[x]) == TRUE) {
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121 qecb$Site[x] <- "EGMP_PasEmsembert"
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122 } else if (grepl(pattern = "Brée-les-Bains", qecb$Site[x]) == TRUE) {
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123 qecb$Site[x] <- "EGMP_BreeBains"
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124 } else if (grepl(pattern = "Antiochat", qecb$Site[x]) == TRUE) {
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125 qecb$Site[x] <- "EGMP_PerreAntiochat"
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126 } else if (grepl(pattern = "Chassiron", qecb$Site[x]) == TRUE) {
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127 qecb$Site[x] <- "EGMP_Chassiron"
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128 } else if (grepl(pattern = "zone p", qecb$Site[x]) == TRUE) {
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129 qecb$Site[x] <- "BASQ_FlotsBleusZP"
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130 } else if (grepl(pattern = "zone f", qecb$Site[x]) == TRUE) {
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131 qecb$Site[x] <- "BASQ_FlotsBleusZF"
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132 } else if (grepl(pattern = "Saint-Michel", qecb$Site[x]) == TRUE) {
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133 qecb$Site[x] <- "GONB_IlotStMichel"
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134 } else if (grepl(pattern = "Quéménès", qecb$Site[x]) == TRUE) {
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135 qecb$Site[x] <- "FINS_Quemenes"
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136 } else if (grepl(pattern = "Goulenez", qecb$Site[x]) == TRUE) {
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137 qecb$Site[x] <- "FINS_SeinGoulenez"
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138 } else if (grepl(pattern = "Kilaourou", qecb$Site[x]) == TRUE) {
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139 qecb$Site[x] <- "FINS_SeinKilaourou"
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140 } else if (grepl(pattern = "Verdelet", qecb$Site[x]) == TRUE) {
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141 qecb$Site[x] <- "ARMO_Verdelet"
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142 } else if (grepl(pattern = "Piégu", qecb$Site[x]) == TRUE) {
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143 qecb$Site[x] <- "ARMO_Piegu"
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144 } else if (grepl(pattern = "Bilfot", qecb$Site[x]) == TRUE) {
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145 qecb$Site[x] <- "ARMO_Bilfot"
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146 } else if (grepl(pattern = "Plate", qecb$Site[x]) == TRUE) {
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147 qecb$Site[x] <- "ARMO_IlePlate"
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148 } else if (grepl(pattern = "Perharidy", qecb$Site[x]) == TRUE) {
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149 qecb$Site[x] <- "PDMO_Perharidy"
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150 } else if (grepl(pattern = "Keraliou", qecb$Site[x]) == TRUE) {
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151 qecb$Site[x] <- "BRES_Keraliou"
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152 } else if (grepl(pattern = "Mousterlin", qecb$Site[x]) == TRUE) {
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153 qecb$Site[x] <- "FINS_Mousterlin"
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154 } else if (grepl(pattern = "Nicolas", qecb$Site[x]) == TRUE) {
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155 qecb$Site[x] <- "FINS_StNicolasGlenan"
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156 }
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157 if (grepl(pattern = "Roz", qecb$site[x]) == TRUE) {
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158 qecb$Site[x] <- "FINS_AnseRoz"
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159 }
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160 }
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161
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162 # Name for report/plot
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163
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164 qecb <- tibble::add_column(qecb, Site_bis = qecb$Site, .after = "Site")
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165
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166 qecb$Site_bis <- ifelse(qecb$Site == "GDMO_Locmariaquer", "Locmariaquer", qecb$Site_bis)
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167 qecb$Site_bis <- ifelse(qecb$Site == "GDMO_BegLann", "Beg Lann", qecb$Site_bis)
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168 qecb$Site_bis <- ifelse(qecb$Site == "FOUR_PlateauFour", "Plateau du Four", qecb$Site_bis)
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169 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_GroinCou", "Groin du Cou", qecb$Site_bis)
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170 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_PasEmsembert", "Le Pas d'Emsembert", qecb$Site_bis)
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171 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_BreeBains", "La Brée-les-Bains", qecb$Site_bis)
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172 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_PerreAntiochat", "Le Perré d'Antiochat", qecb$Site_bis)
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173 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_Chassiron", "Chassiron", qecb$Site_bis)
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174 qecb$Site_bis <- ifelse(qecb$Site == "BASQ_FlotsBleusZP", "Les Flots Bleus / zone pêcheurs", qecb$Site_bis)
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175 qecb$Site_bis <- ifelse(qecb$Site == "BASQ_FlotsBleusZF", "Les Flots Bleus / zone familles", qecb$Site_bis)
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176 qecb$Site_bis <- ifelse(qecb$Site == "GONB_IlotStMichel", "Îlot Saint-Michel", qecb$Site_bis)
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177 qecb$Site_bis <- ifelse(qecb$Site == "FINS_Quemenes", "Quéménès", qecb$Site_bis)
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178 qecb$Site_bis <- ifelse(qecb$Site == "FINS_SeinGoulenez", "Île de Sein - Goulenez", qecb$Site_bis)
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179 qecb$Site_bis <- ifelse(qecb$Site == "FINS_SeinKilaourou", "Île de Sein - Kilaourou", qecb$Site_bis)
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180 qecb$Site_bis <- ifelse(qecb$Site == "ARMO_Verdelet", "Îlot du Verdelet", qecb$Site_bis)
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181 qecb$Site_bis <- ifelse(qecb$Site == "ARMO_Piegu", "Piégu", qecb$Site_bis)
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182 qecb$Site_bis <- ifelse(qecb$Site == "ARMO_Bilfot", "Pointe de Bilfot", qecb$Site_bis)
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183 qecb$Site_bis <- ifelse(qecb$Site == "ARMO_IlePlate", "Île Plate", qecb$Site_bis)
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184 qecb$Site_bis <- ifelse(qecb$Site == "PDMO_Perharidy", "Perharidy", qecb$Site_bis)
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185 qecb$Site_bis <- ifelse(qecb$Site == "BRES_Keraliou", "Keraliou", qecb$Site_bis)
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186 qecb$Site_bis <- ifelse(qecb$Site == "FINS_Mousterlin", "Pointe de Mousterlin", qecb$Site_bis)
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187 qecb$Site_bis <- ifelse(qecb$Site == "FINS_StNicolasGlenan", "Saint-Nicolas des Glénan", qecb$Site_bis)
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188 qecb$Site_bis <- ifelse(qecb$Site == "FINS_AnseRoz", "Pointe de l'Anse du Roz", qecb$Site_bis)
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189
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190 ## change some variables to factor
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191
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192 # 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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193 ix <- grep("^X..", names(qecb))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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194 qecb[ix] <- lapply(qecb[ix], as.numeric)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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195 rm(ix)
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196
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197
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198 ## save the final, complete qecb df_
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199
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200 qecb <- qecb[, c(72:107, 1:71)]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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201
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202 ## qecb df preparation prior qecb calculation
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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203
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204 # Several issues to solve in the df first
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205
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206
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207 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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208
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209 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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210
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211 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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212
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213 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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214
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215 # 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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216
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217 qecbnew <- qecb
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218
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219 # df with list object nb and corresponding site_year_month_day value to solve for loop issues
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220
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221 df_list_loop <- data.frame("site_year_month_day" = unique(qecbnew$site_year_month_day),
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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222 "loop nb" = c(1:seq_along(unique(qecbnew$site_year_month_day))))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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223
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224 # 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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225 # 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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226
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227 # list nb (28) - EGMP_BreeBains.2016.04.06
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228 qecbnew$Face <- as.character(qecbnew$Face)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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229 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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230 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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231 qecbnew$Face <- as.factor(qecbnew$Face)
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232
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233 # list nb 33 - EGMP_PerreAntiochat.2016.04.07
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234 qecbnew$Face <- as.character(qecbnew$Face)
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235 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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236 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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237 qecbnew$Face <- as.factor(qecbnew$Face)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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238
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239 # list nb 37 - EGMP_Chassiron.2016.03.09
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240 qecbnew$Face <- as.character(qecbnew$Face)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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241 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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242 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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243 qecbnew$Face <- as.factor(qecbnew$Face)
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244
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245 # list nb 76 - ARMO_Verdelet.2015.03.23
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246 qecbnew$Face <- as.character(qecbnew$Face)
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247 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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248 qecbnew$Face <- as.factor(qecbnew$Face)
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249
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250 # list nb 116 - "GDMO_Locmariaquer.2018.09.10"
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251 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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252 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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253 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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254 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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255 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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256
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257 # 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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258
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259 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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260 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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261 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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262 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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263 rm(df_list_loop, qecb_i)
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264
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265
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266 # 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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267
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268 # first for Spirobranchus
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269
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270 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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271 qecbnew$Nb.Spirobranchus.lamarckii.total <- as.character(qecbnew$Nb.Spirobranchus.lamarckii.total)
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272
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273
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274 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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275 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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276 (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$Nb.Spirobranchus.lamarckii.5B))[, c("site_year_month_day", "Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total")])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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277
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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278 quemenes <- dplyr::filter(qecbnew, Site == "FINS_Quemenes")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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279 quemenes <- dplyr::arrange(quemenes, date_fiche)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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280 # for Quemenes, issue because for sampling date "FINS_Quemenes.2015.09.30" the 5 counts of Spirobranchus were encoded in 1B instead of total !!! I noticed this issue when mining data (see below), therefore I corrected before running below script for Spirobranchus.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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281 qecbnew$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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282
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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283 (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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284 rm(quemenes)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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285
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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286 seinkilaourou <- dplyr::filter(qecbnew, Site == "FINS_SeinKilaourou")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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287 seinkilaourou <- dplyr::arrange(seinkilaourou, date_fiche)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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288 # same issue with SeinKilaourou
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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289 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$Nb.Spirobranchus.lamarckii.total)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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290 (seinkilaourou <- dplyr::filter(qecbnew, site_year_month_day == "FINS_SeinKilaourou.2015.04.21")[, c("site_year_month_day", "Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total")])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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291 rm(seinkilaourou)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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292
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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293 # some more issues however with "x100"count data
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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294 spirobranchus <- subset(qecbnew, !is.na(qecbnew$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$Nb.Spirobranchus.lamarckii.total))[, c("site_year_month_day", "Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total")]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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295
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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296 for (i in c(1:nrow(spirobranchus))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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297 spirobranchus$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
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298 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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299
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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300 spirobranchus$mean.x.100 <- unlist(spirobranchus$mean.x.100)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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301 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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302 for (i in c(1:nrow(spirobranchus))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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303 spirobranchus$diff[[i]] <- spirobranchus[i, "Nb.Spirobranchus.lamarckii.total"] - spirobranchus[i, "mean.x.100"]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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304 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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305
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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306 spirobranchus$diff <- abs(as.integer(spirobranchus$diff))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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307 spirobranchus <- dplyr::arrange(spirobranchus, desc(diff), mean.x.100)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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308 spirobranchus <- dplyr::arrange(dplyr::filter(spirobranchus, diff != 0 & mean.x.100 != 0), desc(diff))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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309
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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310 # check it all in the qecbnew df
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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311
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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312 for (i in c(1:nrow(qecbnew))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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313 qecbnew$mean.x.100[[i]] <-
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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314 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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315 } # 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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316 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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317
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318
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319 for (i in c(1:nrow(qecbnew))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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320 qecbnew$mean.x.100[[i]] <- ifelse(qecbnew$mean.x.100[[i]] == "NaN", NA, qecbnew$mean.x.100[[i]])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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321 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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322 qecbnew$mean.x.100 <- as.integer(qecbnew$mean.x.100)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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323
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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324 qecbnew$Nb.Spirobranchus.lamarckii.total <- as.integer(qecbnew$Nb.Spirobranchus.lamarckii.total)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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325 qecbnew$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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326 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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327 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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328 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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329
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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330 qecbnew$Nb.Spirobranchus.lamarckii.total <- ifelse(qecbnew$Nb.Spirobranchus.lamarckii.total.diff != 0 & qecbnew$mean.x.100 != 0, qecbnew$mean.x.100, qecbnew$Nb.Spirobranchus.lamarckii.total)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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331 spirobranchus_diff <- qecbnew[, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total", "Nb.Spirobranchus.lamarckii.total.ini", "mean.x.100", "Nb.Spirobranchus.lamarckii.total.diff")]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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332 spirobranchus_diff$Nb.Spirobranchus.lamarckii.total.diff <- abs(as.integer(spirobranchus_diff$Nb.Spirobranchus.lamarckii.total.diff))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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333 spirobranchus_diff <- dplyr::arrange(spirobranchus_diff, desc(Nb.Spirobranchus.lamarckii.total.diff), mean.x.100)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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334 spirobranchus_diff <- dplyr::arrange(dplyr::filter(spirobranchus_diff, Nb.Spirobranchus.lamarckii.total.diff != 0 & mean.x.100 != 0), desc(Nb.Spirobranchus.lamarckii.total.diff))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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335 # ok, change made when data x 100 was not correct.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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336
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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337 # finally, change NA by mean.x100 for Spirobranchus total
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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338 qecbnew$Nb.Spirobranchus.lamarckii.total <- as.character(qecbnew$Nb.Spirobranchus.lamarckii.total)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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339 for (i in c(1:nrow(qecbnew))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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diff changeset
340 qecbnew$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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341 } # 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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342
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343
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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diff changeset
344 for (i in c(1:nrow(qecbnew))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
345 qecbnew$Nb.Spirobranchus.lamarckii.total[[i]] <- ifelse(qecbnew$Nb.Spirobranchus.lamarckii.total[[i]] == "NaN", NA, qecbnew$Nb.Spirobranchus.lamarckii.total[[i]])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
346 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
347
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
348 qecbnew$Nb.Spirobranchus.lamarckii.total <- as.integer(qecbnew$Nb.Spirobranchus.lamarckii.total)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
349
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
350 qecbnew$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
351 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
352 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
353 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
354
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
355 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
356
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
357 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
358
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
359 # do the same for spirorbis
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
360
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
361 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
362 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
363
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
364 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
365 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
366 (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$Nb.spirorbis.5A))[, c("site_year_month_day", "Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A", "Nb.spirorbis.total")])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
367
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
368 # In contrast to Spirobranchus data, no encoding issues for spirorbis data, cfr when sub-quadrat 1A-5A are ALL encoded, NA for total.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
369
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
370 # some more issues however with "x200"count data
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
371
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
372 spirorbis <- subset(qecbnew, !is.na(qecbnew$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$Nb.spirorbis.total))[, c("site_year_month_day", "Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A", "Nb.spirorbis.total")]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
373 for (i in c(1:nrow(spirorbis))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
374 spirorbis$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
375 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
376 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
377 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
378 for (i in c(1:nrow(spirorbis))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
379 spirorbis$diff[[i]] <- spirorbis[i, "Nb.spirorbis.total"] - spirorbis[i, "mean.x.200"]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
380 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
381 spirorbis$diff <- abs(as.integer(spirorbis$diff))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
382 spirorbis <- dplyr::arrange(spirorbis, desc(diff), mean.x.200)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
383 (gonb_ilotstmichel_2015_04_18 <- dplyr::filter(spirorbis, site_year_month_day == "GONB_IlotStMichel.2015.04.18"))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
384 rm(gonb_ilotstmichel_2015_04_18)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
385 spirorbis <- dplyr::arrange(dplyr::filter(spirorbis, diff != 0 & mean.x.200 != 0), desc(diff))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
386
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
387 # check it all in the qecbnew df
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
388
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
389 for (i in c(1:nrow(qecbnew))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
390 qecbnew$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
391 } # 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
392 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
393
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
394 for (i in c(1:nrow(qecbnew))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
395 qecbnew$mean.x.200[[i]] <- ifelse(qecbnew$mean.x.200[[i]] == "NaN", NA, qecbnew$mean.x.200[[i]])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
396 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
397
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
398 qecbnew$mean.x.200 <- as.integer(qecbnew$mean.x.200)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
399
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
400 qecbnew$Nb.spirorbis.total <- as.integer(qecbnew$Nb.spirorbis.total)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
401 qecbnew$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
402 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
403 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
404 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
405
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
406 qecbnew$Nb.spirorbis.total <- ifelse(qecbnew$Nb.spirorbis.total.diff != 0 & qecbnew$mean.x.200 != 0, qecbnew$mean.x.200, qecbnew$Nb.spirorbis.total)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
407 spirorbis_diff <- qecbnew[, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A", "Nb.spirorbis.total", "Nb.spirorbis.total.ini", "mean.x.200", "Nb.spirorbis.total.diff")]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
408 spirorbis_diff$Nb.spirorbis.total.diff <- abs(as.integer(spirorbis_diff$Nb.spirorbis.total.diff))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
409 spirorbis_diff <- dplyr::arrange(spirorbis_diff, desc(Nb.spirorbis.total.diff), mean.x.200)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
410 spirorbis_diff <- dplyr::arrange(dplyr::filter(spirorbis_diff, Nb.spirorbis.total.diff != 0 & mean.x.200 != 0), desc(Nb.spirorbis.total.diff))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
411 # ok, change made when data x 200 was not correct.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
412
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
413 # finally, change NA by mean.x200 for spirorbis total
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
414 qecbnew$Nb.spirorbis.total <- as.character(qecbnew$Nb.spirorbis.total)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
415 for (i in c(1:nrow(qecbnew))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
416 qecbnew$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
417 } # 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
418
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
419 for (i in c(1:nrow(qecbnew))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
420 qecbnew$Nb.spirorbis.total[[i]] <- ifelse(qecbnew$Nb.spirorbis.total[[i]] == "NaN", NA, qecbnew$Nb.spirorbis.total[[i]])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
421 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
422
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
423 qecbnew$Nb.spirorbis.total <- as.integer(qecbnew$Nb.spirorbis.total)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
424
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
425 qecbnew$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
426 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
427 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
428 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
429
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
430 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
431
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
432 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
433
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 # 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
436
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
437 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
438 qecbnew$X..algues.brunes <- ifelse(qecbnew$X..algues.brunes > 100, 100, qecbnew$X..algues.brunes)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
439 dplyr::filter(qecbnew, X..algues.rouges > 100)[, c("Site", "date_fiche", "Type.Bloc", "Numéro.Bloc.échantillon", "Face", "X..algues.rouges")]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
440 qecbnew$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
441
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 ## 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
444
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
445 # 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
446 # I theregore change these NAs by 0
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
447
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
448 # 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
449 qecbnew[, c("X..algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
450 "X..algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
451 "X..Lithophyllum",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
452 "X..Cladophora",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
453 "Nb.Littorina.obtusata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
454 "Nb.Gibbula.cineraria",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
455 "Nb.Gibbula.pennanti",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
456 "Nb.Gibbula.umbilicalis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
457 "X..Eponges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
458 "X..Ascidies.Coloniales",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
459 "X..Ascidies.Solitaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
460 "X..Bryozoaires.Dresses",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
461 "X..algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
462 "X..Roche.Nue",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
463 "Nb.spirorbis.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
464 "X..Balanes.Vivantes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
465 "Nb.Spirobranchus.lamarckii.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
466 "X..Surface.Accolement")] <- lapply(qecbnew[,
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
467 c("X..algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
468 "X..algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
469 "X..Lithophyllum",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
470 "X..Cladophora",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
471 "Nb.Littorina.obtusata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
472 "Nb.Gibbula.cineraria",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
473 "Nb.Gibbula.pennanti",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
474 "Nb.Gibbula.umbilicalis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
475 "X..Eponges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
476 "X..Ascidies.Coloniales",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
477 "X..Ascidies.Solitaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
478 "X..Bryozoaires.Dresses",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
479 "X..algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
480 "X..Roche.Nue",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
481 "Nb.spirorbis.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
482 "X..Balanes.Vivantes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
483 "Nb.Spirobranchus.lamarckii.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
484 "X..Surface.Accolement")],
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
485 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
486
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
487 # 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
488
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
489 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
490 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
491 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
492
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 # add a region variable
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
495 region <- rep(NA, nrow(qecbnew))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
496 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
497 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
498 rm(region)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
499 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
500
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
501 # accolement function according to recent 'retournement'
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
502
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
503 ## 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
504
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
505 # 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
506
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
507 qecbnew <- tibble::add_column(qecbnew, terri_ = substr(qecbnew$Site, 1, 4), .after = "Site_bis")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
508
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
509 qecbnew$X..Eponges_ini <- qecbnew$X..Eponges
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
510 qecbnew$X..Ascidies.Coloniales_ini <- qecbnew$X..Ascidies.Coloniales
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
511 qecbnew$X..Ascidies.Solitaires_ini <- qecbnew$X..Ascidies.Solitaires
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
512 qecbnew$X..Bryozoaires.Dresses_ini <- qecbnew$X..Bryozoaires.Dresses
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
513 qecbnew$X..Lithophyllum_ini <- qecbnew$X..Lithophyllum
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
514 qecbnew$X..Balanes.Vivantes_ini <- qecbnew$X..Balanes.Vivantes
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
515
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
516 df_bm_fs <- qecbnew %>% dplyr::filter(Type.Bloc == "Bloc mobile" & Face == "face supérieure")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
517 df_bm_fi <- qecbnew %>% dplyr::filter(Type.Bloc == "Bloc mobile" & Face == "face inférieure")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
518 df_bf <- qecbnew %>% dplyr::filter(Type.Bloc != "Bloc mobile")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
519
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
520 `%notin%` <- Negate(`%in%`)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
521
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
522 acco_fct <- function(var_) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
523
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
524 df_bm_fi$var_cor.acco. <<- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
525
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
526 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
527
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
528 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
529 ifelse(#df_$Couleur.dominante %in% c("Rouge", "Brune", "Brune-Rouge") ||
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
530 df_bm_fs$Couleur.dominante[[i]] %in% c("Blanche", "Verte", "Blanche-Verte", "Colorée"), df_bm_fi[i, var_] / (100 - df_bm_fi$X..Surface.Accolement[[i]]) * 100, df_bm_fi[i, var_])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
531 } else {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
532 ifelse(df_bm_fs$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
533 & df_bm_fi$X..Surface.Accolement[[i]] != 0 # I have to use it in dplyr::filter this time as well for EGMP- BASQ (but not for Bretagne, although could be added, same result); identical/repeated measure for BM.FI and BM.FS
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
534 & df_bm_fs$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
535 }
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 # 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
542
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 # apply acco_fct to BM.FI variables
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
545
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
546 apply_acco_fct <- function(var_) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
547
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
548 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
549 pre_ <- as.vector(df_bm_fi[, var_])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
550 acco_fct(var_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
551 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
552 show(sort(df_bm_fi$var_cor., decreasing = TRUE, index.return = FALSE)[1:50])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
553 df_bm_fi$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
554 df_bm_fi$var_cor. <<- ifelse(df_bm_fi$var_cor. > 100, 100, df_bm_fi$var_cor.)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
555 show(sort(df_bm_fi$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
556 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
557 par(mfrow = c(1, 3))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
558 hist(pre_, main = var_, xlab = "pre-corection")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
559 hist(df_bm_fi$var_cor., main = var_, xlab = "post-corection")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
560 hist(df_bm_fi[as.vector(which(abs(as.vector(df_bm_fi$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
561 par(mfrow = c(1, 1))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
562 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
563 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
564
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
565 rm(pre_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
566
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 apply_acco_fct("X..Eponges")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
570 apply_acco_fct("X..Ascidies.Coloniales")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
571 apply_acco_fct("X..Ascidies.Solitaires")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
572 apply_acco_fct("X..Bryozoaires.Dresses")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
573 apply_acco_fct("X..Lithophyllum")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
574 apply_acco_fct("X..Balanes.Vivantes")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
575
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
576 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
577 qecbnew <- dplyr::bind_rows(qecbnew, df_bf)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
578
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
579 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
580
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
581 # do remove some more data ...
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
582 # "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
583 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
584
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
585 # save the final qecbnew df_
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
586
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
587 qecb <- qecbnew
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
588
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 `%notin%` <- Negate(`%in%`)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
591
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
592 ## reorder and/or create new variables
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
593
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
594 # 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
595 qecb <- tibble::add_column(qecb, qecb$site_year_month_day, .after = "Site_bis")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
596 qecb <- qecb[, -which(names(qecb) %in% c("site_year_month_day"))]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
597 qecb <- dplyr::rename(qecb, site_year_month_day = `qecb$site_year_month_day`)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
598
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
599 # 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
600 period <- rep(NA, nrow(qecb))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
601 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
602 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
603 qecb$period <- as.factor(qecb$period)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
604 rm(period)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
605
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
606 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
607
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
608 # 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
609 # 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
610
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
611 ## SCRIPT I - NAs <- 0
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
612
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
613 # 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
614
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
615 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
616 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
617 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
618 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
619
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
620 # 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
621
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
622 bretagne_bm[, c(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
623 "X..algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
624 "Strate.algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
625 "X..algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
626 "Strate.algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
627 "X..algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
628 "Strate.algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
629 "X..Cladophora",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
630 "X..Lithophyllum",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
631 "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
632 #"Type.Sediment",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
633 "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
634 "Nb.Littorina.obtusata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
635 "Nb.Gibbula.cineraria",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
636 "Nb.Gibbula.pennanti",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
637 "Nb.Gibbula.umbilicalis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
638 "Nb.Phallusia.mamillata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
639 "Nb.Tethya.aurantium",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
640 #"Nb.Spirobranchus.lamarckii.1B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
641 #"Nb.Spirobranchus.lamarckii.2B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
642 #"Nb.Spirobranchus.lamarckii.3B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
643 #"Nb.Spirobranchus.lamarckii.4B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
644 #"Nb.Spirobranchus.lamarckii.5B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
645 "Nb.Spirobranchus.lamarckii.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
646 #"Nb.spirorbis.1A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
647 #"Nb.spirorbis.2A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
648 #"Nb.spirorbis.3A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
649 #"Nb.spirorbis.4A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
650 #"Nb.spirorbis.5A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
651 "Nb.spirorbis.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
652 #.."Nb.Crassostrea.gigas",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
653 #.."Nb.Ostrea.edulis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
654 #.."X..Mytilus.sp.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
655 #.."X..Hermelles",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
656 #.."X..Hydraires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
657 "X..Eponges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
658 "X..Ascidies.Coloniales",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
659 "X..Ascidies.Solitaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
660 "X..Bryozoaires.Dresses",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
661 "X..Balanes.Vivantes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
662 #"Commentaires.Avant",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
663 "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
664 #"Type.sustrat.observé",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
665 #"Commentaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
666 "Nb.Cancer.pagurus..Tourteau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
667 "Nb.Necora.puber..Etrille.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
668 "Nb.Carcinus.maenas..Crabe.vert.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
669 "Nb.Nucella.lapilus..Pourpre.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
670 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
671 #.."Nb.Octopus.vulgaris..Poulpe.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
672 "Nb.Galathea..Galathées.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
673 #.."Nb.Paracentrotus.lividus..Oursin.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
674 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
675 "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
676 "Nb.Haliotis.tuberculata..Ormeau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
677 #"Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
678 "Nb.Littorina.littorea..Bigorneau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
679 "Nb.Xantho.pilipes..Xanthe.poilu.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
680 "Nb.Mimachlamys.varia..Pétoncle.noir."
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
681 )
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
682 ] <- lapply(bretagne_bm[, c(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
683 "X..algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
684 "Strate.algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
685 "X..algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
686 "Strate.algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
687 "X..algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
688 "Strate.algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
689 "X..Cladophora",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
690 "X..Lithophyllum",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
691 "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
692 #"Type.Sediment",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
693 "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
694 "Nb.Littorina.obtusata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
695 "Nb.Gibbula.cineraria",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
696 "Nb.Gibbula.pennanti",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
697 "Nb.Gibbula.umbilicalis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
698 "Nb.Phallusia.mamillata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
699 "Nb.Tethya.aurantium",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
700 #"Nb.Spirobranchus.lamarckii.1B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
701 #"Nb.Spirobranchus.lamarckii.2B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
702 #"Nb.Spirobranchus.lamarckii.3B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
703 #"Nb.Spirobranchus.lamarckii.4B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
704 #"Nb.Spirobranchus.lamarckii.5B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
705 "Nb.Spirobranchus.lamarckii.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
706 #"Nb.spirorbis.1A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
707 #"Nb.spirorbis.2A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
708 #"Nb.spirorbis.3A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
709 #"Nb.spirorbis.4A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
710 #"Nb.spirorbis.5A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
711 "Nb.spirorbis.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
712 #.."Nb.Crassostrea.gigas",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
713 #.."Nb.Ostrea.edulis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
714 #.."X..Mytilus.sp.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
715 #.."X..Hermelles",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
716 #.."X..Hydraires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
717 "X..Eponges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
718 "X..Ascidies.Coloniales",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
719 "X..Ascidies.Solitaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
720 "X..Bryozoaires.Dresses",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
721 "X..Balanes.Vivantes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
722 #"Commentaires.Avant",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
723 "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
724 #"Type.sustrat.observé",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
725 #"Commentaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
726 "Nb.Cancer.pagurus..Tourteau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
727 "Nb.Necora.puber..Etrille.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
728 "Nb.Carcinus.maenas..Crabe.vert.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
729 "Nb.Nucella.lapilus..Pourpre.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
730 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
731 #.."Nb.Octopus.vulgaris..Poulpe.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
732 "Nb.Galathea..Galathées.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
733 #.."Nb.Paracentrotus.lividus..Oursin.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
734 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
735 "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
736 "Nb.Haliotis.tuberculata..Ormeau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
737 #"Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
738 "Nb.Littorina.littorea..Bigorneau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
739 "Nb.Xantho.pilipes..Xanthe.poilu.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
740 "Nb.Mimachlamys.varia..Pétoncle.noir."
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
741 )
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
742 ], 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
743
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 # bretagne_bf
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
746 bretagne_bf[, c(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
747 "X..algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
748 "Strate.algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
749 "X..algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
750 "Strate.algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
751 "X..algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
752 "Strate.algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
753 "X..Cladophora",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
754 "X..Lithophyllum",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
755 "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
756 #"Type.Sediment",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
757 "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
758 "Nb.Littorina.obtusata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
759 "Nb.Gibbula.cineraria",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
760 "Nb.Gibbula.pennanti",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
761 "Nb.Gibbula.umbilicalis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
762 "Nb.Phallusia.mamillata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
763 "Nb.Tethya.aurantium",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
764 #"Nb.Spirobranchus.lamarckii.1B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
765 #"Nb.Spirobranchus.lamarckii.2B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
766 #"Nb.Spirobranchus.lamarckii.3B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
767 #"Nb.Spirobranchus.lamarckii.4B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
768 #"Nb.Spirobranchus.lamarckii.5B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
769 "Nb.Spirobranchus.lamarckii.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
770 #"Nb.spirorbis.1A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
771 #"Nb.spirorbis.2A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
772 #"Nb.spirorbis.3A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
773 #"Nb.spirorbis.4A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
774 #"Nb.spirorbis.5A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
775 "Nb.spirorbis.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
776 #.."Nb.Crassostrea.gigas",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
777 #.."Nb.Ostrea.edulis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
778 #.."X..Mytilus.sp.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
779 #.."X..Hermelles",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
780 #.."X..Hydraires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
781 "X..Eponges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
782 "X..Ascidies.Coloniales",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
783 "X..Ascidies.Solitaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
784 "X..Bryozoaires.Dresses",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
785 "X..Balanes.Vivantes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
786 #"Commentaires.Avant",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
787 "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
788 #"Type.sustrat.observé",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
789 #"Commentaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
790 #."Nb.Cancer.pagurus..Tourteau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
791 #.."Nb.Necora.puber..Etrille.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
792 #."Nb.Carcinus.maenas..Crabe.vert.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
793 #."Nb.Nucella.lapilus..Pourpre.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
794 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
795 #.."Nb.Octopus.vulgaris..Poulpe.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
796 #."Nb.Galathea..Galathées.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
797 #.."Nb.Paracentrotus.lividus..Oursin.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
798 #."Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
799 #."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
800 #."Nb.Haliotis.tuberculata..Ormeau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
801 #."Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
802 #."Nb.Littorina.littorea..Bigorneau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
803 #."Nb.Xantho.pilipes..Xanthe.poilu.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
804 #."Nb.Mimachlamys.varia..Pétoncle.noir."
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
805 )
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
806 ] <- lapply(bretagne_bf[, c(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
807 "X..algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
808 "Strate.algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
809 "X..algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
810 "Strate.algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
811 "X..algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
812 "Strate.algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
813 "X..Cladophora",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
814 "X..Lithophyllum",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
815 "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
816 #"Type.Sediment",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
817 "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
818 "Nb.Littorina.obtusata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
819 "Nb.Gibbula.cineraria",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
820 "Nb.Gibbula.pennanti",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
821 "Nb.Gibbula.umbilicalis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
822 "Nb.Phallusia.mamillata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
823 "Nb.Tethya.aurantium",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
824 #"Nb.Spirobranchus.lamarckii.1B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
825 #"Nb.Spirobranchus.lamarckii.2B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
826 #"Nb.Spirobranchus.lamarckii.3B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
827 #"Nb.Spirobranchus.lamarckii.4B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
828 #"Nb.Spirobranchus.lamarckii.5B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
829 "Nb.Spirobranchus.lamarckii.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
830 #"Nb.spirorbis.1A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
831 #"Nb.spirorbis.2A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
832 #"Nb.spirorbis.3A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
833 #"Nb.spirorbis.4A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
834 #"Nb.spirorbis.5A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
835 "Nb.spirorbis.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
836 #.."Nb.Crassostrea.gigas",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
837 #.."Nb.Ostrea.edulis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
838 #.."X..Mytilus.sp.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
839 #.."X..Hermelles",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
840 #.."X..Hydraires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
841 "X..Eponges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
842 "X..Ascidies.Coloniales",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
843 "X..Ascidies.Solitaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
844 "X..Bryozoaires.Dresses",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
845 "X..Balanes.Vivantes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
846 #"Commentaires.Avant",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
847 "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
848 #"Type.sustrat.observé",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
849 #"Commentaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
850 #."Nb.Cancer.pagurus..Tourteau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
851 #.."Nb.Necora.puber..Etrille.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
852 #."Nb.Carcinus.maenas..Crabe.vert.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
853 #."Nb.Nucella.lapilus..Pourpre.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
854 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
855 #.."Nb.Octopus.vulgaris..Poulpe.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
856 #."Nb.Galathea..Galathées.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
857 #.."Nb.Paracentrotus.lividus..Oursin.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
858 #."Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
859 #."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
860 #."Nb.Haliotis.tuberculata..Ormeau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
861 #."Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
862 #."Nb.Littorina.littorea..Bigorneau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
863 #."Nb.Xantho.pilipes..Xanthe.poilu.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
864 #."Nb.Mimachlamys.varia..Pétoncle.noir."
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
865 )
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
866 ], 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
867
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 # egmp_basq_bm
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
870 egmp_basq_bm[, c(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
871 "X..algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
872 "Strate.algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
873 "X..algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
874 "Strate.algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
875 "X..algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
876 "Strate.algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
877 "X..Cladophora",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
878 "X..Lithophyllum",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
879 "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
880 #"Type.Sediment",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
881 "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
882 "Nb.Littorina.obtusata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
883 "Nb.Gibbula.cineraria",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
884 "Nb.Gibbula.pennanti",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
885 "Nb.Gibbula.umbilicalis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
886 "Nb.Phallusia.mamillata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
887 "Nb.Tethya.aurantium",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
888 #"Nb.Spirobranchus.lamarckii.1B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
889 #"Nb.Spirobranchus.lamarckii.2B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
890 #"Nb.Spirobranchus.lamarckii.3B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
891 #"Nb.Spirobranchus.lamarckii.4B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
892 #"Nb.Spirobranchus.lamarckii.5B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
893 "Nb.Spirobranchus.lamarckii.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
894 #"Nb.spirorbis.1A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
895 #"Nb.spirorbis.2A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
896 #"Nb.spirorbis.3A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
897 #"Nb.spirorbis.4A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
898 #"Nb.spirorbis.5A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
899 "Nb.spirorbis.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
900 "Nb.Crassostrea.gigas",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
901 "Nb.Ostrea.edulis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
902 "X..Mytilus.sp.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
903 "X..Hermelles",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
904 "X..Hydraires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
905 "X..Eponges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
906 "X..Ascidies.Coloniales",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
907 "X..Ascidies.Solitaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
908 "X..Bryozoaires.Dresses",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
909 "X..Balanes.Vivantes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
910 #"Commentaires.Avant",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
911 "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
912 #"Type.sustrat.observé",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
913 #"Commentaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
914 "Nb.Cancer.pagurus..Tourteau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
915 "Nb.Necora.puber..Etrille.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
916 "Nb.Carcinus.maenas..Crabe.vert.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
917 "Nb.Nucella.lapilus..Pourpre.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
918 "Nb.Eriphia.verrucosa..Crabe.verruqueux.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
919 "Nb.Octopus.vulgaris..Poulpe.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
920 "Nb.Galathea..Galathées.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
921 "Nb.Paracentrotus.lividus..Oursin.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
922 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
923 "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
924 "Nb.Haliotis.tuberculata..Ormeau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
925 "Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
926 "Nb.Littorina.littorea..Bigorneau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
927 "Nb.Xantho.pilipes..Xanthe.poilu.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
928 "Nb.Mimachlamys.varia..Pétoncle.noir."
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
929 )
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
930 ] <- lapply(egmp_basq_bm[, c(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
931 "X..algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
932 "Strate.algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
933 "X..algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
934 "Strate.algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
935 "X..algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
936 "Strate.algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
937 "X..Cladophora",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
938 "X..Lithophyllum",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
939 "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
940 #"Type.Sediment",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
941 "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
942 "Nb.Littorina.obtusata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
943 "Nb.Gibbula.cineraria",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
944 "Nb.Gibbula.pennanti",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
945 "Nb.Gibbula.umbilicalis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
946 "Nb.Phallusia.mamillata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
947 "Nb.Tethya.aurantium",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
948 #"Nb.Spirobranchus.lamarckii.1B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
949 #"Nb.Spirobranchus.lamarckii.2B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
950 #"Nb.Spirobranchus.lamarckii.3B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
951 #"Nb.Spirobranchus.lamarckii.4B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
952 #"Nb.Spirobranchus.lamarckii.5B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
953 "Nb.Spirobranchus.lamarckii.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
954 #"Nb.spirorbis.1A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
955 #"Nb.spirorbis.2A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
956 #"Nb.spirorbis.3A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
957 #"Nb.spirorbis.4A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
958 #"Nb.spirorbis.5A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
959 "Nb.spirorbis.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
960 "Nb.Crassostrea.gigas",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
961 "Nb.Ostrea.edulis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
962 "X..Mytilus.sp.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
963 "X..Hermelles",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
964 "X..Hydraires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
965 "X..Eponges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
966 "X..Ascidies.Coloniales",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
967 "X..Ascidies.Solitaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
968 "X..Bryozoaires.Dresses",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
969 "X..Balanes.Vivantes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
970 #"Commentaires.Avant",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
971 "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
972 #"Type.sustrat.observé",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
973 #"Commentaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
974 "Nb.Cancer.pagurus..Tourteau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
975 "Nb.Necora.puber..Etrille.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
976 "Nb.Carcinus.maenas..Crabe.vert.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
977 "Nb.Nucella.lapilus..Pourpre.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
978 "Nb.Eriphia.verrucosa..Crabe.verruqueux.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
979 "Nb.Octopus.vulgaris..Poulpe.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
980 "Nb.Galathea..Galathées.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
981 "Nb.Paracentrotus.lividus..Oursin.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
982 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
983 "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
984 "Nb.Haliotis.tuberculata..Ormeau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
985 "Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
986 "Nb.Littorina.littorea..Bigorneau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
987 "Nb.Xantho.pilipes..Xanthe.poilu.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
988 "Nb.Mimachlamys.varia..Pétoncle.noir."
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
989 )
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
990 ], 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
991
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 # egmp_basq_bf
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
994 egmp_basq_bf[, c(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
995 "X..algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
996 "Strate.algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
997 "X..algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
998 "Strate.algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
999 "X..algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1000 "Strate.algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1001 "X..Cladophora",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1002 "X..Lithophyllum",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1003 "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
1004 #"Type.Sediment",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1005 "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
1006 "Nb.Littorina.obtusata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1007 "Nb.Gibbula.cineraria",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1008 "Nb.Gibbula.pennanti",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1009 "Nb.Gibbula.umbilicalis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1010 "Nb.Phallusia.mamillata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1011 "Nb.Tethya.aurantium",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1012 #"Nb.Spirobranchus.lamarckii.1B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1013 #"Nb.Spirobranchus.lamarckii.2B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1014 #"Nb.Spirobranchus.lamarckii.3B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1015 #"Nb.Spirobranchus.lamarckii.4B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1016 #"Nb.Spirobranchus.lamarckii.5B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1017 "Nb.Spirobranchus.lamarckii.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1018 #"Nb.spirorbis.1A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1019 #"Nb.spirorbis.2A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1020 #"Nb.spirorbis.3A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1021 #"Nb.spirorbis.4A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1022 #"Nb.spirorbis.5A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1023 "Nb.spirorbis.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1024 "Nb.Crassostrea.gigas",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1025 "Nb.Ostrea.edulis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1026 "X..Mytilus.sp.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1027 "X..Hermelles",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1028 "X..Hydraires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1029 "X..Eponges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1030 "X..Ascidies.Coloniales",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1031 "X..Ascidies.Solitaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1032 "X..Bryozoaires.Dresses",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1033 "X..Balanes.Vivantes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1034 #"Commentaires.Avant",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1035 "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
1036 #"Type.sustrat.observé",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1037 #"Commentaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1038 #."Nb.Cancer.pagurus..Tourteau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1039 #.."Nb.Necora.puber..Etrille.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1040 #."Nb.Carcinus.maenas..Crabe.vert.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1041 #."Nb.Nucella.lapilus..Pourpre.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1042 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1043 #.."Nb.Octopus.vulgaris..Poulpe.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1044 #."Nb.Galathea..Galathées.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1045 #.."Nb.Paracentrotus.lividus..Oursin.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1046 #."Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1047 #."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
1048 #."Nb.Haliotis.tuberculata..Ormeau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1049 #."Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1050 #."Nb.Littorina.littorea..Bigorneau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1051 #."Nb.Xantho.pilipes..Xanthe.poilu.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1052 #."Nb.Mimachlamys.varia..Pétoncle.noir."
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1053 )
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1054 ] <- lapply(egmp_basq_bf[, c(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1055 "X..algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1056 "Strate.algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1057 "X..algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1058 "Strate.algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1059 "X..algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1060 "Strate.algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1061 "X..Cladophora",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1062 "X..Lithophyllum",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1063 "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
1064 #"Type.Sediment",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1065 "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
1066 "Nb.Littorina.obtusata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1067 "Nb.Gibbula.cineraria",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1068 "Nb.Gibbula.pennanti",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1069 "Nb.Gibbula.umbilicalis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1070 "Nb.Phallusia.mamillata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1071 "Nb.Tethya.aurantium",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1072 #"Nb.Spirobranchus.lamarckii.1B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1073 #"Nb.Spirobranchus.lamarckii.2B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1074 #"Nb.Spirobranchus.lamarckii.3B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1075 #"Nb.Spirobranchus.lamarckii.4B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1076 #"Nb.Spirobranchus.lamarckii.5B",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1077 "Nb.Spirobranchus.lamarckii.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1078 #"Nb.spirorbis.1A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1079 #"Nb.spirorbis.2A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1080 #"Nb.spirorbis.3A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1081 #"Nb.spirorbis.4A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1082 #"Nb.spirorbis.5A",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1083 "Nb.spirorbis.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1084 "Nb.Crassostrea.gigas",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1085 "Nb.Ostrea.edulis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1086 "X..Mytilus.sp.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1087 "X..Hermelles",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1088 "X..Hydraires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1089 "X..Eponges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1090 "X..Ascidies.Coloniales",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1091 "X..Ascidies.Solitaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1092 "X..Bryozoaires.Dresses",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1093 "X..Balanes.Vivantes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1094 #"Commentaires.Avant",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1095 "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
1096 #"Type.sustrat.observé",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1097 #"Commentaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1098 #."Nb.Cancer.pagurus..Tourteau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1099 #.."Nb.Necora.puber..Etrille.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1100 #."Nb.Carcinus.maenas..Crabe.vert.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1101 #."Nb.Nucella.lapilus..Pourpre.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1102 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1103 #.."Nb.Octopus.vulgaris..Poulpe.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1104 #."Nb.Galathea..Galathées.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1105 #.."Nb.Paracentrotus.lividus..Oursin.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1106 #."Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1107 #."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
1108 #."Nb.Haliotis.tuberculata..Ormeau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1109 #."Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1110 #."Nb.Littorina.littorea..Bigorneau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1111 #."Nb.Xantho.pilipes..Xanthe.poilu.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1112 #."Nb.Mimachlamys.varia..Pétoncle.noir."
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1113 )
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1114 ], 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
1115
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 # merge dfs.
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1118 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
1119 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
1120 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
1121
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1122 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
1123
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1124 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
1125
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 ## analyse matricielle
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1128
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1129 # 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
1130
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1131 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
1132
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 numero_quadrat <- stringr::str_sub(qecbnato0$quadrat_bis, start = -1)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1135 qecbnato0 <- tibble::add_column(qecbnato0, numero_quadrat, .after = "quadrat_bis")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1136 rm(numero_quadrat)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1137 qecbnato0$numero_quadrat <- as.integer(qecbnato0$numero_quadrat)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1138
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1139
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1140 qecbnato0$Year <- as.integer(qecbnato0$Year)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1141 qecbnato0$Month <- as.integer(qecbnato0$Month)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1142 qecbnato0$Day <- as.integer(qecbnato0$Day)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1143
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 # 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
1147 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
1148 ############################################################
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 # 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
1151
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1152 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
1153 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
1154
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1155 saveRDS(qecbnato0, "qecbnato0.RDS")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1156
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 # Start dissimilarity calculation with some data handling #
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1161 # #
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 # 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
1165
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1166 bret_egmp_basq_qecb <- c(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1167 "X..algues.brunes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1168 "X..algues.rouges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1169 "X..algues.vertes",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1170 "X..Cladophora",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1171 "X..Lithophyllum",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1172 "Nb.Littorina.obtusata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1173 "Nb.Gibbula.cineraria",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1174 "Nb.Gibbula.pennanti",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1175 "Nb.Gibbula.umbilicalis",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1176 "Nb.Phallusia.mamillata",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1177 "Nb.Tethya.aurantium",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1178 "Nb.Spirobranchus.lamarckii.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1179 "Nb.spirorbis.total",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1180 "X..Eponges",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1181 "X..Ascidies.Coloniales",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1182 "X..Ascidies.Solitaires",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1183 "X..Bryozoaires.Dresses",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1184 "X..Balanes.Vivantes"
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1185 #, "X..Recouvrement.Sediment"
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1186 #, "X..Roche.Nue"
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1187 #, "X..Surface.Accolement"
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1188 )
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 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
1191
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1192 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
1193 "Nb.Necora.puber..Etrille.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1194 "Nb.Carcinus.maenas..Crabe.vert.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1195 "Nb.Nucella.lapilus..Pourpre.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1196 "Nb.Galathea..Galathées.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1197 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1198 "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
1199 "Nb.Haliotis.tuberculata..Ormeau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1200 "Nb.Littorina.littorea..Bigorneau.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1201 "Nb.Xantho.pilipes..Xanthe.poilu.",
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1202 "Nb.Mimachlamys.varia..Pétoncle.noir.")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1203
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1204 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
1205
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1206 # 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
1207 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
1208 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
1209
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 # Compute dissimilarity #
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1214 # #
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 ### 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
1217
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1218 # loop in a fct
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1219
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1220 matri_fct_bmf <- function(data, conca) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1221
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1222 matri_df <- data
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1223
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1224 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
1225
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1226 qecbnato0_x <- matri_df %>% dplyr::filter(site_year_month_day == unique(matri_df$site_year_month_day)[[x]])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1227
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1228 rownames(qecbnato0_x) <- paste0(qecbnato0_x$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
1229
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 mtxdis <- vegan::vegdist(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1232 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
1233
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1234 na.rm = TRUE,
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1235 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
1236 )
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 #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
1240 # mtxdis <- ecole::bray0(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1241 # sqrt
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1242 # (qecbnato0_x[,conca]), na.rm = TRUE)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1243
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1244 expand.grid(mtxdis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1245
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1246 mtxdisdf_ <- as.data.frame(as.matrix(mtxdis))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1247
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1248 a_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1249 b_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1250 c_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1251 d_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1252 e_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1253 f_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1254 g_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1255 h_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1256 i_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1257 j_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1258 k_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1259 l_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1260 m_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1261 n_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1262
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1263 for (z in c(1:nrow(mtxdisdf_))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1264
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1265 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
1266 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
1267 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
1268 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
1269 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
1270 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
1271 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
1272 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
1273 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
1274 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
1275 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
1276 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
1277 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
1278 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
1279
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 rm(z)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1283
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1284 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
1285 a_ <- a_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1286 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
1287 b_ <- b_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1288 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
1289 c_ <- c_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1290 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
1291 d_ <- d_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1292 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
1293 e_ <- e_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1294 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
1295 f_ <- f_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1296 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
1297 g_ <- g_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1298 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
1299 h_ <- h_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1300 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
1301 i_ <- i_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1302 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
1303 j_ <- j_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1304 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
1305 k_ <- k_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1306 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
1307 l_ <- l_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1308 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
1309 m_ <- m_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1310 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
1311 n_ <- n_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1312
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1313 rm(y)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1314
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1315 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
1316 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
1317 names(df_) <- c("dist.", "name_")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1318
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1319 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
1320 rm(name_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1321
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1322 q_ <- strsplit(df_$name_, " & ")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1323 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
1324 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
1325 df_ <- dplyr::bind_cols(df_, q_df_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1326
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1327 rm(q_, mat_, q_df_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1328
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1329 split_ <- strsplit(df_$V1, "_")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1330 v1_split_ <- as.data.frame(matrix(unlist(split_), ncol = 4, byrow = TRUE))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1331 split_ <- strsplit(df_$V2, "_")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1332 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
1333
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1334 df_ <- dplyr::bind_cols(df_, v1_split_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1335 df_ <- dplyr::bind_cols(df_, v2_split_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1336 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
1337 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
1338
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1339 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
1340
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1341 rm(split_, v1_split_, v2_split_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1342 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
1343
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1344 matri_list[[x]] <- df_red_
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1345 matri_list <<- matri_list
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1346
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1347 rm(df_red_, qecbnato0_x, x)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1348
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 matri_df <- do.call("rbind", matri_list)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1352
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1353 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
1354
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1355 matri_df <<- matri_df
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1356
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1357 hist(matri_df$dist.)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1358
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 data_ <- dplyr::filter(qecbnato0, Face == "face supérieure")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1362 data_$Type.Bloc <- ifelse(as.character(data_$Type.Bloc) == "Roche en place", "Bloc fixé", as.character(data_$Type.Bloc))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1363 matri_list <- vector("list", length(unique(data_$site_year_month_day)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1364
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1365 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
1366 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
1367
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1368 matri_full_bm_bf_fs <- matri_df
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1369
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 rm(data_, matri_df, matri_list)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1372
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 ### 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
1375
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1376 # loop in a fct
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1377
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1378 matri_fct_bmm <- function(data, conca) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1379
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1380 matri_df <- data
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1381
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1382 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
1383
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1384 qecbnato0_x <- matri_df %>% dplyr::filter(site_year_month_day == unique(matri_df$site_year_month_day)[[x]])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1385
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1386 rownames(qecbnato0_x) <- paste0(qecbnato0_x$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
1387
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 mtxdis <- vegan::vegdist(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1390 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
1391 na.rm = TRUE,
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1392 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
1393 )
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 #mtxdis <- ecole::bray0(
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1397 # sqrt(qecbnato0_x[, conca]), na.rm = TRUE)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1398
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 expand.grid(mtxdis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1401
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1402 mtxdisdf_ <- as.data.frame(as.matrix(mtxdis))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1403
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1404 a_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1405 b_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1406 c_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1407 d_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1408 e_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1409 f_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1410 g_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1411 h_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1412 i_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1413 j_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1414 k_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1415 l_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1416 m_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1417 n_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1418 o_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1419 p_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1420 q_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1421 r_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1422 s_ <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1423
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1424 for (z in c(1:nrow(mtxdisdf_))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1425
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1426 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
1427 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
1428 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
1429 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
1430 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
1431 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
1432 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
1433 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
1434 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
1435 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
1436 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
1437 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
1438 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
1439 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
1440 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
1441 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
1442 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
1443 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
1444 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
1445
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 rm(z)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1449
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1450 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
1451 a_ <- a_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1452 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
1453 b_ <- b_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1454 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
1455 c_ <- c_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1456 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
1457 d_ <- d_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1458 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
1459 e_ <- e_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1460 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
1461 f_ <- f_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1462 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
1463 g_ <- g_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1464 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
1465 h_ <- h_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1466 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
1467 i_ <- i_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1468 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
1469 j_ <- j_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1470 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
1471 k_ <- k_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1472 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
1473 l_ <- l_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1474 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
1475 m_ <- m_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1476 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
1477 n_ <- n_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1478 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
1479 o_ <- o_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1480 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
1481 p_ <- p_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1482 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
1483 q_ <- q_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1484 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
1485 r_ <- r_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1486 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
1487 s_ <- s_[1:y]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1488
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1489 rm(y)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1490
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1491 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
1492 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
1493 names(df_) <- c("dist.", "name_")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1494
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1495 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
1496 rm(name_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1497
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1498 q_ <- strsplit(df_$name_, " & ")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1499 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
1500 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
1501 df_ <- dplyr::bind_cols(df_, q_df_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1502
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1503 rm(q_, mat_, q_df_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1504
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1505 split_ <- strsplit(df_$V1, "_")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1506 v1_split_ <- as.data.frame(matrix(unlist(split_), ncol = 4, byrow = TRUE))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1507 split_ <- strsplit(df_$V2, "_")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1508 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
1509
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1510 df_ <- dplyr::bind_cols(df_, v1_split_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1511 df_ <- dplyr::bind_cols(df_, v2_split_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1512 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
1513 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
1514
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1515 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
1516
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1517 rm(split_, v1_split_, v2_split_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1518 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
1519
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1520 matri_list[[x]] <- df_red_
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1521 matri_list <<- matri_list
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1522
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1523 rm(df_red_, qecbnato0_x, x)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1524
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 matri_df <- do.call("rbind", matri_list)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1528
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1529 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
1530
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1531 matri_df <<- matri_df
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1532
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1533 hist(matri_df$dist.)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1534
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 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
1538 matri_list <- vector("list", length(unique(data_$site_year_month_day)))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1539
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1540 matri_fct_bmm(data = data_, conca = c(bret_egmp_basq_qecb, egmp_basq_qecb))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1541 hist(matri_df$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
1542
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1543 matri_full_bm_bf_fi <- matri_df
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1544
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1545 rm(data_, matri_df, matri_list)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1546
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 # Plot dissimilarity #
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1551 # #
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 ## plot
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1554
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1555 # activate line
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1556
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1557 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
1558 matri_full_bm_bf_fs$Site <- paste0(matri_full_bm_bf_fs$departement, "_", matri_full_bm_bf_fs$Site)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1559 matri_full_bm_bf_fs <- subset(matri_full_bm_bf_fs, select = - c(departement))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1560
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1561 matri_full_bm_bf_fs <- tibble::add_column(matri_full_bm_bf_fs, Date = as.Date(paste0(matri_full_bm_bf_fs$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
1562 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
1563
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1564 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
1565 matri_full_bm_bf_fi$Site <- paste0(matri_full_bm_bf_fi$departement, "_", matri_full_bm_bf_fi$Site)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1566 matri_full_bm_bf_fi <- subset(matri_full_bm_bf_fi, select = - c(departement))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1567 matri_full_bm_bf_fi <- tibble::add_column(matri_full_bm_bf_fi, Date = as.Date(paste0(matri_full_bm_bf_fi$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
1568 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
1569
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1570 # 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
1571
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 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
1574 ggplot2::geom_boxplot() +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1575 #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
1576 ggplot2::xlab("") +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1577 ggplot2::ylab("distance diss. BM.BF_FS") +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1578 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
1579
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1580 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
1581
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1582 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
1583 ggplot2::geom_boxplot() +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1584 #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
1585 ggplot2::xlab("") +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1586 ggplot2::ylab("distance diss. BM_FS.FI") +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1587 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
1588
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1589 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
1590
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1591 # 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
1592 matri_full_bm_bf_fs$Quadrat <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1593 for (i in c(1:seq_len(nrow(matri_full_bm_bf_fs)))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1594 ifelse(matri_full_bm_bf_fs$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
1595 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1596 matri_full_bm_bf_fs$Numéro.Bloc <- NA
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1597 for (i in c(1:seq_len(nrow(matri_full_bm_bf_fs)))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1598 ifelse(matri_full_bm_bf_fs$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
1599 }
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 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$Numéro.Bloc), .after = "site_year_month_day")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1602 matri_full_bm_bf_fi <- tibble::add_column(matri_full_bm_bf_fi, site_year_month_day.q_BMnb = paste0(matri_full_bm_bf_fi$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
1603
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1604 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
1605 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
1606 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
1607 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
1608
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1609 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
1610
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1611 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
1612 matri_full$Site <- paste0(matri_full$departement, "_", matri_full$Site)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1613 matri_full <- subset(matri_full, select = - c(departement))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1614 matri_full <- tibble::add_column(matri_full, Date = as.Date(paste0(matri_full$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
1615
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1616 # Name for report/plot
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1617
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1618 matri_full <- tibble::add_column(matri_full, Site_bis = matri_full$Site, .after = "Site")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1619
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1620 matri_full$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
1621 matri_full$Site_bis <- ifelse(matri_full$Site == "GDMO_BegLann", "Beg Lann", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1622 matri_full$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
1623 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_GroinCou", "Groin du Cou", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1624 matri_full$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
1625 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_BreeBains", "La Brée-les-Bains", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1626 matri_full$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
1627 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_Chassiron", "Chassiron", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1628 matri_full$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
1629 matri_full$Site_bis <- ifelse(matri_full$Site == "BASQ_FlotsBleusZF", "Les Flots Bleus / zone familles", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1630 matri_full$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
1631 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_Quemenes", "Quéménès", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1632 matri_full$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
1633 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_SeinKilaourou", "Île de Sein - Kilaourou", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1634 matri_full$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
1635 matri_full$Site_bis <- ifelse(matri_full$Site == "ARMO_Piegu", "Piégu", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1636 matri_full$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
1637 matri_full$Site_bis <- ifelse(matri_full$Site == "ARMO_IlePlate", "Île Plate", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1638 matri_full$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
1639 matri_full$Site_bis <- ifelse(matri_full$Site == "BRES_Keraliou", "Keraliou", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1640 matri_full$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
1641 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_StNicolasGlenan", "Saint-Nicolas des Glénan", matri_full$Site_bis)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1642 matri_full$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
1643
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1644 saveRDS(matri_full, "matri_full.RDS")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1645
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 # Plot the dissimilarity per site #
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1649 # #
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 ## plot dissimilarity coefficient
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1652
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1653 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
1654 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
1655 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
1656
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 ## 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
1659
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1660 # Stats
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1661
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1662 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
1663
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1664 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
1665
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1666 # Quality scale based on quartiles
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1667
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1668 if (choice == "N") {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1669 one <- round(mean(unlist(dplyr::filter(matri_full, BM_FS.FI_dist. <= quantile(matri_full$BM_FS.FI_dist., 0.25, na.rm = TRUE))["BM_FS.FI_dist."])), digits = 3)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1670 two <- round(mean(unlist(dplyr::filter(matri_full, BM_FS.FI_dist. > quantile(matri_full$BM_FS.FI_dist., 0.25, na.rm = TRUE) & BM_FS.FI_dist. <= quantile(matri_full$BM_FS.FI_dist., 0.5, na.rm = TRUE))["BM_FS.FI_dist."])), digits = 3)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1671 three <- round(mean(unlist(dplyr::filter(matri_full, BM_FS.FI_dist. > quantile(matri_full$BM_FS.FI_dist., 0.5, na.rm = TRUE) & BM_FS.FI_dist. <= quantile(matri_full$BM_FS.FI_dist., 0.75, na.rm = TRUE))["BM_FS.FI_dist."])), digits = 3)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1672 four <- round(mean(unlist(dplyr::filter(matri_full, BM_FS.FI_dist. > quantile(matri_full$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
1673 }else {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1674 one <- 0.47
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1675 two <- 0.7
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1676 three <- 0.83
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1677 four <- 0.98
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1678 }
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 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
1681
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1682 for (i in c(1:length(unique(bm_fs_fi_dist_stat$Site)))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1683
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1684 df1 <- dplyr::filter(bm_fs_fi_dist_stat, bm_fs_fi_dist_stat$Site == unique(bm_fs_fi_dist_stat$Site)[i])
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1685
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1686 bm_fs_fi_plot <- ggplot2::ggplot() +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1687 ggplot2::geom_point(ggplot2::aes(x = bm_fs_fi_dist_stat$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
1688 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
1689 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
1690 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
1691 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
1692 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
1693 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
1694 ggplot2::geom_pointrange(ggplot2::aes(x = df1$Date, y = df1$BM_FS.FI_dist.med, ymin = df1$BM_FS.FI_dist.min, ymax = df1$BM_FS.FI_dist.max), col = "black") +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1695 ggplot2::xlab("Date") +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1696 ggplot2::ylab("Coef dissim BM FS-FI") +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1697 ggplot2::ggtitle(unique(df1$Site_bis)) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1698 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
1699
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1700 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
1701
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 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
1705
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 ## 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
1708
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1709 # Stats
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1710
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1711 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
1712
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1713 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
1714
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1715 # Quality scale based on quartiles
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1716
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1717 if (choice == "N") {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1718 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
1719 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
1720 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
1721 four <- round(mean(unlist(dplyr::filter(matri_full, BM.BF_FS_dist. > quantile(matri_full$BM.BF_FS_dist., 0.75, na.rm = TRUE))["BM.BF_FS_dist."])), digits = 3)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1722
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1723 }else {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1724 one <- 0.19
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1725 two <- 0.32
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1726 three <- 0.455
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1727 four <- 0.735
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1728 }
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1729 # Plot
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1730
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1731 for (i in c(1:length(unique(bm_bf_fs_dist_stat$Site)))) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1732
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1733 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
1734
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1735 bm_bf_fs_plot <- ggplot2::ggplot() +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1736 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
1737 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
1738 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
1739 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
1740 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
1741 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
1742 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
1743 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
1744 ggplot2::xlab("Date") +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1745 ggplot2::ylab("Coef dissim BM-BF FS") +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1746 ggplot2::ggtitle(unique(df1$Site_bis)) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1747 ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, vjust = 0.5, hjust = 1), legend.position = "none")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1748
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
parents:
diff changeset
1749 ggplot2::ggsave(paste0("bm_bf_", df1$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
1750
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 rm(df1, four, i, one, three, two, xmax_, xmin_, ymax_, ymin_)