Mercurial > repos > ecology > cb_ivr

annotate cb_ivr.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"
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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2 # date: "19 April 2021" )
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4 #Rscript
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6 ###############################
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7 ## ##
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8 ###############################
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10 #####Packages : dplyr
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11 # tidyr
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12 # readr
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13 # writexl
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14 # stringr
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15 # readxl
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16 # tibble
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17 # lubridate
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18 # cowplot
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19 # magrittr
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20 # rmarkdown
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21 library(magrittr)
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22 #####Load arguments
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24 args <- commandArgs(trailingOnly = TRUE)
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26 ### Import data
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28 if (length(args) < 1) {
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29 stop("This tool needs at least 1 argument")
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30 }else {
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31 fiche_val <- args[1]
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32 input_data <- args[2]
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34 }
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36 #############################################################
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37 # #
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38 # Load and clean the data #
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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39 # #
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40 #############################################################
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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41 ### load ivr data
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43 ivr <- read.csv2(input_data, header = FALSE, fileEncoding = "Latin1")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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44 names_ <- as.vector(unlist(ivr[1, ]))
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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45 names_ <- gsub(" ", ".", names_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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46 colnames(ivr) <- names_
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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47 ivr <- ivr[-1, ]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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48 ivr <- ivr[, -17]
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50 # NB inversion between id and ID.Fiche variable names
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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51 ivr <- dplyr::rename(ivr, XX = ID.Fiche)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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52 ivr <- dplyr::rename(ivr, ID.Fiche = id)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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53 ivr <- dplyr::rename(ivr, id = XX)
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56 ### load excel files "Fiche terrain" the metadata
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58 fiche <- read.csv2(fiche_val, fileEncoding = "Latin1") # fileEncoding = "Latin1" cfr é in variable names
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60 date_fiche <- as.Date(stringr::str_sub(fiche$date.sortie, end = 10), origin = "1970-01-01")
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61 fiche <- tibble::add_column(fiche, date_fiche, .after = "date.sortie")
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62 rm(date_fiche)
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64 ## ivr vs fiche terrain
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65 ivr$id <- as.numeric(ivr[, c("id")])
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67 fiche_red <- dplyr::filter(fiche, fiche$ID.Fiche %in% unique(ivr[, c("id")]))
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69 id_count <- ivr %>% dplyr::group_by(id) %>% dplyr::count()
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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70 id_count <- dplyr::rename(id_count, "ID.Fiche" = "id")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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71 id_count <- dplyr::ungroup(id_count)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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72 id_count <- as.data.frame(id_count)
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74 fiche_red <- dplyr::left_join(fiche_red, id_count)
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76 # rep fiche terrain information
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77 fiche_expanded <- fiche_red[rep(row.names(fiche_red), fiche_red$n), 1:ncol(fiche_red)]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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78 fiche_expanded <- dplyr::rename(fiche_expanded, "id" = "ID.Fiche")
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80 ## merge ivr data and ficheterrain information
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81 ivr <- dplyr::bind_cols(ivr, fiche_expanded)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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82 ivr <- dplyr::rename(ivr, "id.ivr" = "id...1")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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83 ivr <- dplyr::rename(ivr, "id.fiche" = "id...17")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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85 rm(fiche_expanded, fiche_red, id_count)
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87 ivr <- ivr %>% tidyr::separate(date_fiche, c("Year", "Month", "Day"), sep = "-", remove = FALSE)
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89 ## 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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91 # Name for data analysis
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92 ivr <- tibble::add_column(ivr, Site = ivr$zone.habitat, .after = "ID.Fiche")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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93 ivr$Site <- gsub(pattern = " \\(champ de blocs\\)", replacement = "", ivr$Site)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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94 ivr$Site <- gsub(pattern = " \\(champ blocs\\)", replacement = "", ivr$Site)
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96 for (x in seq_along(ivr$Site)) {
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97 if (grepl(pattern = "Locmariaquer", ivr$Site[x]) == TRUE) {
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98 ivr$Site[x] <- "GDMO_Locmariaquer"
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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99 } else if (grepl(pattern = "Beg Lann", ivr$Site[x]) == TRUE) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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100 ivr$Site[x] <- "GDMO_BegLann"
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101 } else if (grepl(pattern = "Plateau du Four", ivr$Site[x]) == TRUE) {
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102 ivr$Site[x] <- "FOUR_PlateauFour"
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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103 } else if (grepl(pattern = "Grouin", ivr$Site[x]) == TRUE) {
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104 ivr$Site[x] <- "EGMP_GroinCou"
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105 } else if (grepl(pattern = "Ensembert", ivr$Site[x]) == TRUE) {
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ecology
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106 ivr$Site[x] <- "EGMP_PasEmsembert"
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107 } else if (grepl(pattern = "Brée-les-Bains", ivr$Site[x]) == TRUE) {
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108 ivr$Site[x] <- "EGMP_BreeBains"
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109 } else if (grepl(pattern = "Antiochat", ivr$Site[x]) == TRUE) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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110 ivr$Site[x] <- "EGMP_PerreAntiochat"
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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111 } else if (grepl(pattern = "Chassiron", ivr$Site[x]) == TRUE) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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112 ivr$Site[x] <- "EGMP_Chassiron"
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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113 } else if (grepl(pattern = "zone p", ivr$Site[x]) == TRUE) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
ecology
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114 ivr$Site[x] <- "BASQ_FlotsBleusZP"
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115 } else if (grepl(pattern = "zone f", ivr$Site[x]) == TRUE) {
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116 ivr$Site[x] <- "BASQ_FlotsBleusZF"
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117 } else if (grepl(pattern = "Saint-Michel", ivr$Site[x]) == TRUE) {
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118 ivr$Site[x] <- "GONB_IlotStMichel"
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119 } else if (grepl(pattern = "Quéménès", ivr$Site[x]) == TRUE) {
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ecology
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120 ivr$Site[x] <- "FINS_Quemenes"
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121 } else if (grepl(pattern = "Goulenez", ivr$Site[x]) == TRUE) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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122 ivr$Site[x] <- "FINS_SeinGoulenez"
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123 } else if (grepl(pattern = "Kilaourou", ivr$Site[x]) == TRUE) {
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124 ivr$Site[x] <- "FINS_SeinKilaourou"
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125 } else if (grepl(pattern = "Verdelet", ivr$Site[x]) == TRUE) {
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126 ivr$Site[x] <- "ARMO_Verdelet"
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127 } else if (grepl(pattern = "Piégu", ivr$Site[x]) == TRUE) {
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128 ivr$Site[x] <- "ARMO_Piegu"
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129 } else if (grepl(pattern = "Bilfot", ivr$Site[x]) == TRUE) {
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130 ivr$Site[x] <- "ARMO_Bilfot"
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131 } else if (grepl(pattern = "Plate", ivr$Site[x]) == TRUE) {
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132 ivr$Site[x] <- "ARMO_IlePlate"
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133 } else if (grepl(pattern = "Perharidy", ivr$Site[x]) == TRUE) {
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134 ivr$Site[x] <- "PDMO_Perharidy"
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135 } else if (grepl(pattern = "Keraliou", ivr$Site[x]) == TRUE) {
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136 ivr$Site[x] <- "BRES_Keraliou"
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137 } else if (grepl(pattern = "Mousterlin", ivr$Site[x]) == TRUE) {
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138 ivr$Site[x] <- "FINS_Mousterlin"
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139 } else if (grepl(pattern = "Nicolas", ivr$Site[x]) == TRUE) {
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140 ivr$Site[x] <- "FINS_StNicolasGlenan"
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141 }
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142 if (grepl(pattern = "Roz", ivr$site[x]) == TRUE) {
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143 ivr$Site[x] <- "FINS_AnseRoz"
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144 }
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145 }
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146
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147 # Name for report/plot
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148
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149 ivr <- tibble::add_column(ivr, Site_bis = ivr$Site, .after = "Site")
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150
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151 ivr$Site_bis <- ifelse(ivr$Site == "GDMO_Locmariaquer", "Locmariaquer", ivr$Site_bis)
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152 ivr$Site_bis <- ifelse(ivr$Site == "GDMO_BegLann", "Beg Lann", ivr$Site_bis)
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153 ivr$Site_bis <- ifelse(ivr$Site == "FOUR_PlateauFour", "Plateau du Four", ivr$Site_bis)
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154 ivr$Site_bis <- ifelse(ivr$Site == "EGMP_GroinCou", "Grouin du Cou", ivr$Site_bis)
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155 ivr$Site_bis <- ifelse(ivr$Site == "EGMP_PasEmsembert", "Le Pas d'Emsembert", ivr$Site_bis)
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156 ivr$Site_bis <- ifelse(ivr$Site == "EGMP_BreeBains", "La Brée-les-Bains", ivr$Site_bis)
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157 ivr$Site_bis <- ifelse(ivr$Site == "EGMP_PerreAntiochat", "Le Perré d'Antiochat", ivr$Site_bis)
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158 ivr$Site_bis <- ifelse(ivr$Site == "EGMP_Chassiron", "Chassiron", ivr$Site_bis)
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159 ivr$Site_bis <- ifelse(ivr$Site == "BASQ_FlotsBleusZP", "Les Flots Bleus / zone pêcheurs", ivr$Site_bis)
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160 ivr$Site_bis <- ifelse(ivr$Site == "BASQ_FlotsBleusZF", "Les Flots Bleus / zone familles", ivr$Site_bis)
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161 ivr$Site_bis <- ifelse(ivr$Site == "GONB_IlotStMichel", "Îlot Saint-Michel", ivr$Site_bis)
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162 ivr$Site_bis <- ifelse(ivr$Site == "FINS_Quemenes", "Quéménès", ivr$Site_bis)
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163 ivr$Site_bis <- ifelse(ivr$Site == "FINS_SeinGoulenez", "Île de Sein - Goulenez", ivr$Site_bis)
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164 ivr$Site_bis <- ifelse(ivr$Site == "FINS_SeinKilaourou", "Île de Sein - Kilaourou", ivr$Site_bis)
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165 ivr$Site_bis <- ifelse(ivr$Site == "ARMO_Verdelet", "Îlot du Verdelet", ivr$Site_bis)
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166 ivr$Site_bis <- ifelse(ivr$Site == "ARMO_Piegu", "Piégu", ivr$Site_bis)
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167 ivr$Site_bis <- ifelse(ivr$Site == "ARMO_Bilfot", "Pointe de Bilfot", ivr$Site_bis)
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168 ivr$Site_bis <- ifelse(ivr$Site == "ARMO_IlePlate", "Île Plate", ivr$Site_bis)
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169 ivr$Site_bis <- ifelse(ivr$Site == "PDMO_Perharidy", "Perharidy", ivr$Site_bis)
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170 ivr$Site_bis <- ifelse(ivr$Site == "BRES_Keraliou", "Keraliou", ivr$Site_bis)
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171 ivr$Site_bis <- ifelse(ivr$Site == "FINS_Mousterlin", "Pointe de Mousterlin", ivr$Site_bis)
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172 ivr$Site_bis <- ifelse(ivr$Site == "FINS_StNicolasGlenan", "Saint-Nicolas des Glénan", ivr$Site_bis)
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173 ivr$Site_bis <- ifelse(ivr$Site == "FINS_AnseRoz", "Pointe de l'Anse du Roz", ivr$Site_bis)
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174
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175 ## change some variable format to integer
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176 ivr$Nb.Blocs.Non.Retournes <- as.integer(ivr$Nb.Blocs.Non.Retournes)
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177 ivr$Nb.Blocs.Retournes <- as.integer(ivr$Nb.Blocs.Retournes)
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178
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179 ivr$Year <- as.integer(ivr$Year)
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180 ivr$Month <- as.integer(ivr$Month)
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181 ivr$Day <- as.integer(ivr$Day)
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182 ivr$Numero.Quadrat <- as.integer(ivr$Numero.Quadrat)
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183
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184
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185 ## save the final, commplete ivr df.
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186
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187 ivr <- ivr[, c(19:54, 1:18)]
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188
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189
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190 ## percentage of unturned vs overturned boulders and IVR previous 0-5 discrete scale values calculation
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191
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192 # create two new variables first
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193 site_year_month_day <- paste0(ivr$Site, ".", gsub("-", ".", as.character(ivr$date_fiche)))
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194 ivr <- tibble::add_column(ivr, site_year_month_day, .after = "Site_bis")
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195 rm(site_year_month_day)
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196
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197 site_year_month_day_qdnb <- paste0(ivr$Site, ".", gsub("-", ".", as.character(ivr$Date)), ".", ivr$Numero.Quadrat)
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198 ivr <- tibble::add_column(ivr, site_year_month_day_qdnb, .after = "site_year_month_day")
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199 rm(site_year_month_day_qdnb)
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200
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201 ivr <- dplyr::arrange(ivr, Site, Year, Month, Numero.Quadrat)
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202
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203 # remove data with NA value for Nb.Blocs.Retournes & Nb.Blocs.Non.Retournes
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204 ivr_naomit <- ivr %>% dplyr::filter(!is.na(ivr$Nb.Blocs.Retournes))
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205 ivr_naomit <- as.data.frame(ivr_naomit)
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206 colnames(ivr_naomit) <- colnames(ivr)
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207 ivr_naomit <- ivr_naomit %>% dplyr::filter(!is.na(ivr_naomit$Nb.Blocs.Non.Retournes))
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208 ivr_naomit <- as.data.frame(ivr_naomit)
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209
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210 # also remove data with Nb.Blocs.Retournes = 0 & Nb.Blocs.Non.Retournes = 0, cfr equivalent to quadrat with no boulders ... makes no sense to consider quadrat without boulder for ivr determination.
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211 ivr_rm <- dplyr::filter(ivr_naomit, ivr_naomit$Nb.Blocs.Retournes == 0 && ivr_naomit$Nb.Blocs.Non.Retournes == 0)
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212 ivr_naomit <- ivr_naomit %>% dplyr::anti_join(ivr_rm)
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213 rm(ivr_rm)
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214
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215 ivr_val_qu_ <- ivr_naomit
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216
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217
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218
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219 #############################################################
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220 # #
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221 # Calcul of the IVR #
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222 # #
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223 #############################################################
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224
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225 ### Percentage of turned boulder
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226 for (i in 1:nrow(ivr_naomit)) {
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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227 (bm <- sum(ivr_naomit$Nb.Blocs.Non.Retournes[i], ivr_naomit$Nb.Blocs.Retournes[i]))
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228 (ivr_val_qu_$blocs.retournes.fr.[i] <- (ivr_naomit$Nb.Blocs.Retournes[i] / bm) * 100)
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229 (ivr_val_qu_$blocs.non.retournes.fr.[i] <- (ivr_naomit$Nb.Blocs.Non.Retournes[i] / bm) * 100)
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230 }
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231
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232 rm(bm, i)
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233
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234
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235 ivr_val_qu_$blocs.non.retournes.fr. <- ifelse(is.nan(ivr_val_qu_$blocs.non.retournes.fr.), NA, ivr_val_qu_$blocs.non.retournes.fr.)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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236 ivr_val_qu_$blocs.retournes.fr. <- ifelse(is.nan(ivr_val_qu_$blocs.retournes.fr.), NA, ivr_val_qu_$blocs.retournes.fr.)
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237
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238
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239 # ivr for loop by quadrat.
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240 for (i in 1:seq_len(nrow(ivr_val_qu_))) {
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241 if (ivr_val_qu_$Nb.Blocs.Non.Retournes[i] == 0 && ivr_val_qu_$Nb.Blocs.Retournes[i] == 0) {
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242 ivr_ <- NA
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243 }else {
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244 if (ivr_val_qu_$blocs.retournes.fr.[i] < 5) {
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245 ivr_ <- 0
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246 } else if (ivr_val_qu_$blocs.retournes.fr.[i] >= 5 && ivr_val_qu_$blocs.retournes.fr.[i] < 25) {
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247 ivr_ <- 1
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248 } else if (ivr_val_qu_$blocs.retournes.fr.[i] >= 25 && ivr_val_qu_$blocs.retournes.fr.[i] < 45) {
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249 ivr_ <- 2
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250 } else if (ivr_val_qu_$blocs.retournes.fr.[i] >= 45 && ivr_val_qu_$blocs.retournes.fr.[i] < 65) {
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251 ivr_ <- 3
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252 } else if (ivr_val_qu_$blocs.retournes.fr.[i] >= 65 && ivr_val_qu_$blocs.retournes.fr.[i] < 85) {
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253 ivr_ <- 4
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254 } else {
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255 ivr_ <- 5
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256 }
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257
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258 ivr_val_qu_$valeur.ivr_quadrat[i] <- ivr_
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259 }
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260 }
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261
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262 rm(i, ivr_)
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263
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264 # reorder variables for logical purpose
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265 ivr_val_qu_ <- ivr_val_qu_[, c(1:56, 58, 57, 59)]
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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266 indic_full <- ivr_val_qu_
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267 saveRDS(ivr_val_qu_, "ivr_val_qu.RDS")
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268 rm(ivr_naomit)
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269
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270
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271 ## Calculate ivr statistics now
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272 ivr_val_qu_stat_ <- ivr_val_qu_ %>% dplyr::group_by(id.ivr, Site, Site_bis, Year, Month, Day) %>% dplyr::summarize(ivr_moy = mean(valeur.ivr_quadrat), ivr_et = sd(valeur.ivr_quadrat), ivr_med = median(valeur.ivr_quadrat), ivr_min = min(valeur.ivr_quadrat), ivr_max = max(valeur.ivr_quadrat), fr.r.moy = mean(blocs.retournes.fr.), fr.r.et = sd(blocs.retournes.fr.), fr.r.med = median(blocs.retournes.fr.), fr.r.min = min(blocs.retournes.fr.), fr.r.max = max(blocs.retournes.fr.), fr.nr.moy = mean(blocs.non.retournes.fr.), fr.nr.et = sd(blocs.non.retournes.fr.), fr.nr.med = median(blocs.non.retournes.fr.), fr.nr.min = min(blocs.non.retournes.fr.), fr.nr.max = max(blocs.non.retournes.fr.), nb. = dplyr::n())
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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273
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274 Date <- as.Date(paste0(ivr_val_qu_stat_$Year, "-", ivr_val_qu_stat_$Month, "-", ivr_val_qu_stat_$Day), origin = "1970-01-01")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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275 ivr_val_qu_stat_ <- tibble::add_column(ivr_val_qu_stat_, Date, .after = "Site_bis")
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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276 rm(Date)
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277
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278 ivr_val_qu_stat_ <- as.data.frame(ivr_val_qu_stat_)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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279 indic <- ivr_val_qu_stat_
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280
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281
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282 #############################################################
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283 # #
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284 # Plot the IVR per site #
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285 # #
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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286 #############################################################
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287
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288 ## plot ivr (NB: Year, Month, Day variable names are replace by Annee, Mois, Jour, cfr previous label use in the script)
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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289 ivr_val_qu_stat_ <- dplyr::rename(ivr_val_qu_stat_, Annee = Year)
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290 ivr_val_qu_stat_ <- dplyr::rename(ivr_val_qu_stat_, Mois = Month)
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291 ivr_val_qu_stat_ <- dplyr::rename(ivr_val_qu_stat_, Jour = Day)
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292
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293
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294 # new IVR scale with continuous 0 to 5 environmental status levels based on % of overturned boulders /20, plus other site data
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295
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296 for (i in c(1:length(unique(ivr_val_qu_stat_$Site)))) {
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297
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298 ivr_val_eg <- dplyr::filter(ivr_val_qu_stat_, ivr_val_qu_stat_$Site == unique(ivr_val_qu_stat_$Site)[i])
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299
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300 ivr_plot <- ggplot2::ggplot() +
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301 ggplot2::geom_point(ggplot2::aes(x = ivr_val_qu_stat_$Date, y = ivr_val_qu_stat_$fr.r.moy / 20), col = "grey") +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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302 ggplot2::geom_rect(ggplot2::aes(xmin = min(ivr_val_qu_stat_$Date), xmax = max(ivr_val_qu_stat_$Date), ymin = - 0.5, ymax = 5 / 20, fill = "#FF0000"), alpha = 0.3) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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303 ggplot2::geom_rect(ggplot2::aes(xmin = min(ivr_val_qu_stat_$Date), xmax = max(ivr_val_qu_stat_$Date), ymin = 5 / 20, ymax = 25 / 20, fill = "#F59404"), alpha = 0.3) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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304 ggplot2::geom_rect(ggplot2::aes(xmin = min(ivr_val_qu_stat_$Date), xmax = max(ivr_val_qu_stat_$Date), ymin = 25 / 20, ymax = 45 / 20, fill = "#FAFA15"), alpha = 0.3) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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305 ggplot2::geom_rect(ggplot2::aes(xmin = min(ivr_val_qu_stat_$Date), xmax = max(ivr_val_qu_stat_$Date), ymin = 45 / 20, ymax = 65 / 20, fill = "#18E125"), alpha = 0.3) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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306 ggplot2::geom_rect(ggplot2::aes(xmin = min(ivr_val_qu_stat_$Date), xmax = max(ivr_val_qu_stat_$Date), ymin = 65 / 20, ymax = 85 / 20, fill = "#04F5F5"), alpha = 0.3) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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307 ggplot2::geom_rect(ggplot2::aes(xmin = min(ivr_val_qu_stat_$Date), xmax = max(ivr_val_qu_stat_$Date), ymin = 85 / 20, ymax = 5.5, fill = "#1A1AE8"), alpha = 0.3) +
8c6142630659 planemo upload for repository https://github.com/Marie59/champ_blocs commit 8b6fcddd239979c11977472de6cbb349690758c8
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308 ggplot2::scale_fill_manual(values = c("#F59404", "#FAFA15", "#FF0000", "#04F5F5", "#18E125", "#1A1AE8")) +
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309 ggplot2::geom_pointrange(ggplot2::aes(x = ivr_val_eg$Date, y = ivr_val_eg$fr.r.moy / 20, ymin = ivr_val_eg$fr.r.moy / 20 - ivr_val_eg$fr.r.et / 20, ymax = ivr_val_eg$fr.r.moy / 20 + ivr_val_eg$fr.r.et / 20), col = "black") +
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310 ggplot2::xlab("Date") +
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311 ggplot2::ylab("IVR") +
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312 ggplot2::ggtitle(unique(ivr_val_eg$Site_bis)) +
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313 ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, vjust = 0.5, hjust = 1), legend.position = "none")
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314
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315 ggplot2::ggsave(paste0("ivr_", unique(ivr_val_eg$Site), ".png"), ivr_plot, height = 3, width = 3.5)
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318 }
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319
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320 report <- args[3]
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321 loop_file <- source(args[4])