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annotate cb_dissimilarity.r @ 1:eabd2cf09cf0 draft default tip

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planemo upload for repository https://github.com/Marie59/champ_blocs commit 075fd90d1a39ae7912b48549e5537971635b9620
author ecology
date Sat, 18 Mar 2023 16:49:02 +0000
parents a8924f69348d
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a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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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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24 #####Load arguments
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26 args <- commandArgs(trailingOnly = TRUE)
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28 #####Import data
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30 if (length(args) < 1) {
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31 stop("This tool needs at least 1 argument")
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32 }else {
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33 fiche_val <- args[1]
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34 input_data <- args[2]
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35 choice <- args[3]
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36 choice_date <- as.numeric(args[4])
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37 }
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39 #############################################################
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40 # #
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41 # Loading and cleaning data #
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42 # #
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43 #############################################################
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44 # load qecb data
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46 qecb <- read.csv2(input_data, header = TRUE, fileEncoding = "Latin1") # fileEncoding = "Latin1", cfr é in variable names
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48 # import csv files ficheterrain
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50 fiche <- read.csv2(fiche_val, header = TRUE, fileEncoding = "Latin1") # fileEncoding = "Latin1", cfr é in variable names
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52 ## work on "Fiche terrain"
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54 date_fiche <- as.Date(stringr::str_sub(fiche$date.sortie, end = 10), origin = "1970-01-01")
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55 fiche <- tibble::add_column(fiche, date_fiche, .after = "date.sortie")
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56 rm(date_fiche)
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58 ## qecb vs fiche terrain
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60 fiche_red <- dplyr::filter(fiche, fiche$ID.Fiche %in% unique(qecb[, c("id")]))
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62 id_count <- qecb %>% dplyr::group_by(id) %>% dplyr::count()
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63 id_count <- dplyr::rename(id_count, "ID.Fiche" = "id")
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64 id_count <- data.frame(id_count)
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65 fiche_red <- dplyr::left_join(fiche_red, id_count)
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67 # rep fiche terrain information
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68 fiche_expanded <- fiche_red[rep(row.names(fiche_red), fiche_red$n), 1:ncol(fiche_red)]
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69 fiche_expanded <- dplyr::rename(fiche_expanded, "id" = "ID.Fiche")
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71 ## merge qecb data and ficheterrain information
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73 qecb <- dplyr::bind_cols(qecb, fiche_expanded)
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74 qecb <- dplyr::rename(qecb, "id_qecb" = "id...1")
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75 qecb <- dplyr::rename(qecb, "id_fiche" = "id...68")
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77 rm(fiche_expanded, fiche_red, id_count)
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79 qecb <- qecb %>% tidyr::separate(date_fiche, c("Year", "Month", "Day"), sep = "-", remove = FALSE)
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82 ## quadrat nb : in contrast to ivr df, quadrat number is missing for many observations in qecb df ; but from the Numero.Photo variable (boulder photo associated to field data collection), I could get back most missing quadrat numbers
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84 quadrat <- stringr::str_extract(qecb$Numero.Photo, "Q[12345]")
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85 qecb <- tibble::add_column(qecb, quadrat, .after = "Numero.Photo")
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86 rm(quadrat)
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88 # check
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89 quadrat_bis <- rep(NA, length = nrow(qecb))
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90 qecb <- tibble::add_column(qecb, quadrat_bis, .after = "quadrat")
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91 rm(quadrat_bis)
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93 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon %in% c(1, 2) & qecb$Type.Bloc == "Bloc mobile", "Q1", qecb$quadrat_bis)
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94 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon %in% c(3, 4) & qecb$Type.Bloc == "Bloc mobile", "Q2", qecb$quadrat_bis)
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95 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon %in% c(5, 6) & qecb$Type.Bloc == "Bloc mobile", "Q3", qecb$quadrat_bis)
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96 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon %in% c(7, 8) & qecb$Type.Bloc == "Bloc mobile", "Q4", qecb$quadrat_bis)
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97 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon %in% c(9, 10) & qecb$Type.Bloc == "Bloc mobile", "Q5", qecb$quadrat_bis)
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98
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99
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100 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon == 1 & qecb$Type.Bloc %in% c("Bloc fixé", "Roche en place"), "Q1", qecb$quadrat_bis)
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101 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon == 2 & qecb$Type.Bloc %in% c("Bloc fixé", "Roche en place"), "Q2", qecb$quadrat_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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102 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon == 3 & qecb$Type.Bloc %in% c("Bloc fixé", "Roche en place"), "Q3", qecb$quadrat_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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103 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon == 4 & qecb$Type.Bloc %in% c("Bloc fixé", "Roche en place"), "Q4", qecb$quadrat_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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104 qecb$quadrat_bis <- ifelse(qecb$Numéro.Bloc.échantillon == 5 & qecb$Type.Bloc %in% c("Bloc fixé", "Roche en place"), "Q5", qecb$quadrat_bis)
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105
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106 ## I create two new variables for Site names, one for data analysis and one for data reporting. Only works for actual ivr df with 22 sites !
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107
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108 # Name for data analysis
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109
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110 qecb <- tibble::add_column(qecb, Site = qecb$zone.habitat, .after = "ID.Fiche")
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111
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112 for (x in seq_along(qecb$Site)) {
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113 if (grepl(pattern = "Locmariaquer", qecb$Site[x]) == TRUE) {
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114 qecb$Site[x] <- "GDMO_Locmariaquer"
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115 } else if (grepl(pattern = "Beg Lann", qecb$Site[x]) == TRUE) {
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116 qecb$Site[x] <- "GDMO_BegLann"
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117 } else if (grepl(pattern = "Plateau du Four", qecb$Site[x]) == TRUE) {
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118 qecb$Site[x] <- "FOUR_PlateauFour"
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119 } else if (grepl(pattern = "Grouin", qecb$Site[x]) == TRUE) {
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120 qecb$Site[x] <- "EGMP_GroinCou"
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121 } else if (grepl(pattern = "Ensembert", qecb$Site[x]) == TRUE) {
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122 qecb$Site[x] <- "EGMP_PasEmsembert"
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123 } else if (grepl(pattern = "Brée-les-Bains", qecb$Site[x]) == TRUE) {
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124 qecb$Site[x] <- "EGMP_BreeBains"
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125 } else if (grepl(pattern = "Antiochat", qecb$Site[x]) == TRUE) {
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ecology
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126 qecb$Site[x] <- "EGMP_PerreAntiochat"
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127 } else if (grepl(pattern = "Chassiron", qecb$Site[x]) == TRUE) {
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128 qecb$Site[x] <- "EGMP_Chassiron"
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129 } else if (grepl(pattern = "zone p", qecb$Site[x]) == TRUE) {
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ecology
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130 qecb$Site[x] <- "BASQ_FlotsBleusZP"
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131 } else if (grepl(pattern = "zone f", qecb$Site[x]) == TRUE) {
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132 qecb$Site[x] <- "BASQ_FlotsBleusZF"
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133 } else if (grepl(pattern = "Saint-Michel", qecb$Site[x]) == TRUE) {
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134 qecb$Site[x] <- "GONB_IlotStMichel"
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135 } else if (grepl(pattern = "Quéménès", qecb$Site[x]) == TRUE) {
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136 qecb$Site[x] <- "FINS_Quemenes"
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137 } else if (grepl(pattern = "Goulenez", qecb$Site[x]) == TRUE) {
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138 qecb$Site[x] <- "FINS_SeinGoulenez"
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139 } else if (grepl(pattern = "Kilaourou", qecb$Site[x]) == TRUE) {
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140 qecb$Site[x] <- "FINS_SeinKilaourou"
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141 } else if (grepl(pattern = "Verdelet", qecb$Site[x]) == TRUE) {
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142 qecb$Site[x] <- "ARMO_Verdelet"
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143 } else if (grepl(pattern = "Piégu", qecb$Site[x]) == TRUE) {
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144 qecb$Site[x] <- "ARMO_Piegu"
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145 } else if (grepl(pattern = "Bilfot", qecb$Site[x]) == TRUE) {
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146 qecb$Site[x] <- "ARMO_Bilfot"
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147 } else if (grepl(pattern = "Plate", qecb$Site[x]) == TRUE) {
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148 qecb$Site[x] <- "ARMO_IlePlate"
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149 } else if (grepl(pattern = "Perharidy", qecb$Site[x]) == TRUE) {
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150 qecb$Site[x] <- "PDMO_Perharidy"
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151 } else if (grepl(pattern = "Keraliou", qecb$Site[x]) == TRUE) {
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152 qecb$Site[x] <- "BRES_Keraliou"
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153 } else if (grepl(pattern = "Mousterlin", qecb$Site[x]) == TRUE) {
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154 qecb$Site[x] <- "FINS_Mousterlin"
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155 } else if (grepl(pattern = "Nicolas", qecb$Site[x]) == TRUE) {
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156 qecb$Site[x] <- "FINS_StNicolasGlenan"
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157 }
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158 if (grepl(pattern = "Roz", qecb$site[x]) == TRUE) {
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159 qecb$Site[x] <- "FINS_AnseRoz"
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160 }
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161 }
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162
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163 # Name for report/plot
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164
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165 qecb <- tibble::add_column(qecb, Site_bis = qecb$Site, .after = "Site")
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166
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167 qecb$Site_bis <- ifelse(qecb$Site == "GDMO_Locmariaquer", "Locmariaquer", qecb$Site_bis)
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168 qecb$Site_bis <- ifelse(qecb$Site == "GDMO_BegLann", "Beg Lann", qecb$Site_bis)
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169 qecb$Site_bis <- ifelse(qecb$Site == "FOUR_PlateauFour", "Plateau du Four", qecb$Site_bis)
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170 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_GroinCou", "Groin du Cou", qecb$Site_bis)
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171 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_PasEmsembert", "Le Pas d'Emsembert", qecb$Site_bis)
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172 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_BreeBains", "La Brée-les-Bains", qecb$Site_bis)
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173 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_PerreAntiochat", "Le Perré d'Antiochat", qecb$Site_bis)
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174 qecb$Site_bis <- ifelse(qecb$Site == "EGMP_Chassiron", "Chassiron", qecb$Site_bis)
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175 qecb$Site_bis <- ifelse(qecb$Site == "BASQ_FlotsBleusZP", "Les Flots Bleus / zone pêcheurs", qecb$Site_bis)
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176 qecb$Site_bis <- ifelse(qecb$Site == "BASQ_FlotsBleusZF", "Les Flots Bleus / zone familles", qecb$Site_bis)
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177 qecb$Site_bis <- ifelse(qecb$Site == "GONB_IlotStMichel", "Îlot Saint-Michel", qecb$Site_bis)
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178 qecb$Site_bis <- ifelse(qecb$Site == "FINS_Quemenes", "Quéménès", qecb$Site_bis)
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179 qecb$Site_bis <- ifelse(qecb$Site == "FINS_SeinGoulenez", "Île de Sein - Goulenez", qecb$Site_bis)
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180 qecb$Site_bis <- ifelse(qecb$Site == "FINS_SeinKilaourou", "Île de Sein - Kilaourou", qecb$Site_bis)
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181 qecb$Site_bis <- ifelse(qecb$Site == "ARMO_Verdelet", "Îlot du Verdelet", qecb$Site_bis)
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182 qecb$Site_bis <- ifelse(qecb$Site == "ARMO_Piegu", "Piégu", qecb$Site_bis)
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183 qecb$Site_bis <- ifelse(qecb$Site == "ARMO_Bilfot", "Pointe de Bilfot", qecb$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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184 qecb$Site_bis <- ifelse(qecb$Site == "ARMO_IlePlate", "Île Plate", qecb$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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185 qecb$Site_bis <- ifelse(qecb$Site == "PDMO_Perharidy", "Perharidy", qecb$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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186 qecb$Site_bis <- ifelse(qecb$Site == "BRES_Keraliou", "Keraliou", qecb$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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187 qecb$Site_bis <- ifelse(qecb$Site == "FINS_Mousterlin", "Pointe de Mousterlin", qecb$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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188 qecb$Site_bis <- ifelse(qecb$Site == "FINS_StNicolasGlenan", "Saint-Nicolas des Glénan", qecb$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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189 qecb$Site_bis <- ifelse(qecb$Site == "FINS_AnseRoz", "Pointe de l'Anse du Roz", qecb$Site_bis)
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190
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191 ## change some variables to factor
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192
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193 # change 'X..' variables that are indeed % to numeric; https://stackoverflow.com/questions/59410939/apply-function-to-all-variables-with-string-in-name
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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194 ix <- grep("^X..", names(qecb))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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195 qecb[ix] <- lapply(qecb[ix], as.numeric)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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196 rm(ix)
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197
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198
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199 ## save the final, complete qecb df_
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200
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201 qecb <- qecb[, c(72:107, 1:71)]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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202
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203 ## qecb df preparation prior qecb calculation
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204
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205 # Several issues to solve in the df first
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206
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207
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208 qecb$Type.Bloc <- factor(qecb$Type.Bloc, levels = c("Bloc mobile", "Bloc fixé", "Roche en place"))
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209
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210 qecb$Face <- factor(qecb$Face, levels = c("face supérieure", "face inférieure"))
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211
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212 qecb <- dplyr::arrange(qecb, Type.Bloc, Face, Numéro.Bloc.échantillon)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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213
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214 qecb <- tibble::add_column(qecb, site_year_month_day = paste0(qecb$Site, ".", qecb$Year, ".", qecb$Month, ".", qecb$Day), .after = "Site_bis")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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215
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216 # save qecb as a new df_ for analysis purpose => several changes to operate to run the code and functions
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217
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218 qecbnew <- qecb
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219
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220 # df with list object nb and corresponding site_year_month_day value to solve for loop issues
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221
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222 df_list_loop <- data.frame("site_year_month_day" = unique(qecbnew$site_year_month_day),
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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223 "loop nb" = c(1:seq_along(unique(qecbnew$site_year_month_day))))
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224
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225 # dplyr::filter for df that makes problem, then eventually correct in the dataframe for wrong coding; brackets (xx) for nb because will change when qecb df_ enlarged.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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226 # these listed boulder field survey error when highlighted when running the loop, that ran into an error ; it was a step by step procedure with solving one listed observation after another when issues appeared. Surely not the best way to proceed, maybe better just to skip these surveys (site + date), but in the present case I wanted to keep most of the observations, therefore I corrected them manually whenever needed.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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227
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228 # list nb (28) - EGMP_BreeBains.2016.04.06
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229 qecbnew$Face <- as.character(qecbnew$Face)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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230 qecbnew$Face <- ifelse(qecbnew$ID.Fiche == "BDD_IVR&QECB_La Bree_20160406_VImport.xlsx" & qecbnew$Référence.bloc == "avr16-LaBreeB9sup", "face supérieure", qecbnew$Face)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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231 qecbnew$Face <- ifelse(qecbnew$ID.Fiche == "BDD_IVR&QECB_La Bree_20160406_VImport.xlsx" & qecbnew$Référence.bloc == "avr16-LaBreeB10sup", "face supérieure", qecbnew$Face)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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232 qecbnew$Face <- as.factor(qecbnew$Face)
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233
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234 # list nb 33 - EGMP_PerreAntiochat.2016.04.07
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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235 qecbnew$Face <- as.character(qecbnew$Face)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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236 qecbnew$Face <- ifelse(qecbnew$ID.Fiche == "BDD_IVR&QECB_PerAnt_20160407_VImport.xlsx" & qecbnew$Référence.bloc == "avr16-PerAntB9sup", "face supérieure", qecbnew$Face)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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237 qecbnew$Face <- ifelse(qecbnew$ID.Fiche == "BDD_IVR&QECB_PerAnt_20160407_VImport.xlsx" & qecbnew$Référence.bloc == "avr16-PerAntB10sup", "face supérieure", qecbnew$Face)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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238 qecbnew$Face <- as.factor(qecbnew$Face)
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239
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240 # list nb 37 - EGMP_Chassiron.2016.03.09
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241 qecbnew$Face <- as.character(qecbnew$Face)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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242 qecbnew$Face <- ifelse(qecbnew$ID.Fiche == "BDD_IVR&QECB_Chassiron_20160309&10_VImport.xlsx" & qecbnew$Référence.bloc == "mars16-ChassB9sup", "face supérieure", qecbnew$Face)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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243 qecbnew$Face <- ifelse(qecbnew$ID.Fiche == "BDD_IVR&QECB_Chassiron_20160309&10_VImport.xlsx" & qecbnew$Référence.bloc == "mars16-ChasB10sup", "face supérieure", qecbnew$Face)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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244 qecbnew$Face <- as.factor(qecbnew$Face)
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245
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246 # list nb 76 - ARMO_Verdelet.2015.03.23
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247 qecbnew$Face <- as.character(qecbnew$Face)
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248 qecbnew$Face <- ifelse(qecbnew$ID.Fiche == "BDD_IVR&QECB_Verdelet_20150323_VImport.xlsx" & qecbnew$Référence.bloc == "mar15-VerB10inf", "face inférieure", qecbnew$Face)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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249 qecbnew$Face <- as.factor(qecbnew$Face)
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250
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251 # list nb 116 - "GDMO_Locmariaquer.2018.09.10"
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252 qecbnew$Type.Bloc <- as.character(qecbnew$Type.Bloc)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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253 qecbnew$Type.Bloc <- ifelse(qecbnew$ID.Fiche == "2018-09-10-GDMO-CDB-001" & qecbnew$Numero.Photo == "2018-09-10_GDMO_01_CDB-5_sup_392578.jpg", "Roche en place", qecbnew$Type.Bloc)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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254 qecbnew$Type.Bloc <- as.factor(qecbnew$Type.Bloc)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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255 qecbnew$quadrat_bis <- ifelse(qecbnew$ID.Fiche == "2018-09-10-GDMO-CDB-001" & qecbnew$Numero.Photo == "2018-09-10_GDMO_01_CDB-5_sup_392578.jpg", "Q5", qecbnew$quadrat_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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256 qecbnew <- qecbnew %>% dplyr::filter(!(ID.Fiche == "2018-09-10-GDMO-CDB-001" & Numero.Photo == ""))
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257
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258 # Few sites to remove prior running the for loop because it was not just a encoding mistake for one data, but a globally wroing coding for the site + date survey.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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259
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260 qecb_i <- qecbnew %>% dplyr::filter(site_year_month_day == "FINS_StNicolasGlenan.2016.04.08") # no bloc fixe !
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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261 qecbnew <- qecbnew %>% dplyr::filter(site_year_month_day != "FINS_StNicolasGlenan.2016.04.08")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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262 qecb_i <- qecbnew %>% dplyr::filter(site_year_month_day == "GDMO_Locmariaquer.2019.09.30") # most faces of blocs mobiles do not correspond to each other; only 3 over 10 boulder have data for both face supérieure and face inférieure
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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263 qecbnew <- qecbnew %>% dplyr::filter(site_year_month_day != "GDMO_Locmariaquer.2019.09.30")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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264 rm(df_list_loop, qecb_i)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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265
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266
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267 # check for species with count within sub-0.1m^2-quadrat (i.e. reduced size quadrat compare to most organisms on boulder to count them, because abundant ; then some extrapolation)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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268
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269 # first for Spirobranchus
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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270
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271 qecbnew$Nb.Spirobranchus.lamarckii.total.ini <- qecbnew$Nb.Spirobranchus.lamarckii.total
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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272 qecbnew$Nb.Spirobranchus.lamarckii.total <- as.character(qecbnew$Nb.Spirobranchus.lamarckii.total)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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273
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274
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275 qecbnew_spirobranchus <- (dplyr::filter(qecbnew, Nb.Spirobranchus.lamarckii.total %in% c(NA, "NaN", "Inf", "-Inf")))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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276 qecbnew_spirobranchus[, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B")] <- sapply(qecbnew_spirobranchus[, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B")], as.character)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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277 (spirobranchus_data <- subset(qecbnew_spirobranchus, !is.na(qecbnew_spirobranchus$Nb.Spirobranchus.lamarckii.1B) || !is.na(qecbnew_spirobranchus$Nb.Spirobranchus.lamarckii.2B) || !is.na(qecbnew_spirobranchus$Nb.Spirobranchus.lamarckii.3B) || !is.na(qecbnew_spirobranchus$Nb.Spirobranchus.lamarckii.4B) || !is.na(qecbnew_spirobranchus$Nb.Spirobranchus.lamarckii.5B))[, c("site_year_month_day", "Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total")])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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278
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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279 quemenes <- dplyr::filter(qecbnew, Site == "FINS_Quemenes")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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280 quemenes <- dplyr::arrange(quemenes, date_fiche)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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281 # for Quemenes, issue because for sampling date "FINS_Quemenes.2015.09.30" the 5 counts of Spirobranchus were encoded in 1B instead of total !!! I noticed this issue when mining data (see below), therefore I corrected before running below script for Spirobranchus.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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282 qecbnew$Nb.Spirobranchus.lamarckii.total <- ifelse(qecbnew$site_year_month_day == "FINS_Quemenes.2015.09.30" & is.na(qecbnew$Nb.Spirobranchus.lamarckii.total), qecbnew$Nb.Spirobranchus.lamarckii.1B, qecbnew$Nb.Spirobranchus.lamarckii.total)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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283
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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284 (quemenes <- dplyr::filter(qecbnew, site_year_month_day == "FINS_Quemenes.2015.09.30")[, c("site_year_month_day", "Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total")])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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285 rm(quemenes)
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286
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287 seinkilaourou <- dplyr::filter(qecbnew, Site == "FINS_SeinKilaourou")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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288 seinkilaourou <- dplyr::arrange(seinkilaourou, date_fiche)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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289 # same issue with SeinKilaourou
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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290 qecbnew$Nb.Spirobranchus.lamarckii.total <- ifelse(qecbnew$site_year_month_day == "FINS_SeinKilaourou.2015.04.21" & is.na(qecbnew$Nb.Spirobranchus.lamarckii.total), qecbnew$Nb.Spirobranchus.lamarckii.1B, qecbnew$Nb.Spirobranchus.lamarckii.total)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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291 (seinkilaourou <- dplyr::filter(qecbnew, site_year_month_day == "FINS_SeinKilaourou.2015.04.21")[, c("site_year_month_day", "Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total")])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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292 rm(seinkilaourou)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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293
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294 # some more issues however with "x100"count data
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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295 spirobranchus <- subset(qecbnew, !is.na(qecbnew$Nb.Spirobranchus.lamarckii.1B) & !is.na(qecbnew$Nb.Spirobranchus.lamarckii.2B) & !is.na(qecbnew$Nb.Spirobranchus.lamarckii.3B) & !is.na(qecbnew$Nb.Spirobranchus.lamarckii.4B) & !is.na(qecbnew$Nb.Spirobranchus.lamarckii.5B) & !is.na(qecbnew$Nb.Spirobranchus.lamarckii.total))[, c("site_year_month_day", "Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total")]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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296
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297 for (i in c(1:nrow(spirobranchus))) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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298 spirobranchus$mean.x.100[[i]] <- sum(spirobranchus[i, c(2:6)], na.rm = TRUE) / sum(!is.na(spirobranchus[i, c(2:6)])) * 100
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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299 }
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300
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301 spirobranchus$mean.x.100 <- unlist(spirobranchus$mean.x.100)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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302 spirobranchus$Nb.Spirobranchus.lamarckii.total <- as.numeric(spirobranchus$Nb.Spirobranchus.lamarckii.total)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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303 for (i in c(1:nrow(spirobranchus))) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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304 spirobranchus$diff[[i]] <- spirobranchus[i, "Nb.Spirobranchus.lamarckii.total"] - spirobranchus[i, "mean.x.100"]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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305 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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306
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307 spirobranchus$diff <- abs(as.integer(spirobranchus$diff))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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308 spirobranchus <- dplyr::arrange(spirobranchus, desc(diff), mean.x.100)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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309 spirobranchus <- dplyr::arrange(dplyr::filter(spirobranchus, diff != 0 & mean.x.100 != 0), desc(diff))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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310
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311 # check it all in the qecbnew df
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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312
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313 for (i in c(1:nrow(qecbnew))) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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314 qecbnew$mean.x.100[[i]] <-
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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315 sum(qecbnew[i, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B")], na.rm = TRUE) / sum(!is.na(qecbnew[i, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B")])) * 100
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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316 } # sum of only NAs/0 = NaN; so replace NaN by Na
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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317 qecbnew$mean.x.100 <- as.character(qecbnew$mean.x.100)
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318
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319
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320 for (i in c(1:nrow(qecbnew))) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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321 qecbnew$mean.x.100[[i]] <- ifelse(qecbnew$mean.x.100[[i]] == "NaN", NA, qecbnew$mean.x.100[[i]])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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322 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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323 qecbnew$mean.x.100 <- as.integer(qecbnew$mean.x.100)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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324
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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325 qecbnew$Nb.Spirobranchus.lamarckii.total <- as.integer(qecbnew$Nb.Spirobranchus.lamarckii.total)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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326 qecbnew$Nb.Spirobranchus.lamarckii.total.diff <- abs((qecbnew$Nb.Spirobranchus.lamarckii.total - qecbnew$mean.x.100))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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diff changeset
327 spirobranchus_diff <- qecbnew[, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total", "Nb.Spirobranchus.lamarckii.total.ini", "mean.x.100", "Nb.Spirobranchus.lamarckii.total.diff")]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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328 spirobranchus_diff <- dplyr::arrange(spirobranchus_diff, desc(Nb.Spirobranchus.lamarckii.total.diff), mean.x.100)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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329 spirobranchus_diff <- dplyr::arrange(dplyr::filter(spirobranchus_diff, Nb.Spirobranchus.lamarckii.total.diff != 0 & mean.x.100 != 0), desc(Nb.Spirobranchus.lamarckii.total.diff))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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330
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
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331 qecbnew$Nb.Spirobranchus.lamarckii.total <- ifelse(qecbnew$Nb.Spirobranchus.lamarckii.total.diff != 0 & qecbnew$mean.x.100 != 0, qecbnew$mean.x.100, qecbnew$Nb.Spirobranchus.lamarckii.total)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
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332 spirobranchus_diff <- qecbnew[, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total", "Nb.Spirobranchus.lamarckii.total.ini", "mean.x.100", "Nb.Spirobranchus.lamarckii.total.diff")]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
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333 spirobranchus_diff$Nb.Spirobranchus.lamarckii.total.diff <- abs(as.integer(spirobranchus_diff$Nb.Spirobranchus.lamarckii.total.diff))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
334 spirobranchus_diff <- dplyr::arrange(spirobranchus_diff, desc(Nb.Spirobranchus.lamarckii.total.diff), mean.x.100)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
335 spirobranchus_diff <- dplyr::arrange(dplyr::filter(spirobranchus_diff, Nb.Spirobranchus.lamarckii.total.diff != 0 & mean.x.100 != 0), desc(Nb.Spirobranchus.lamarckii.total.diff))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
336 # ok, change made when data x 100 was not correct.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
337
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
338 # finally, change NA by mean.x100 for Spirobranchus total
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
339 qecbnew$Nb.Spirobranchus.lamarckii.total <- as.character(qecbnew$Nb.Spirobranchus.lamarckii.total)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
340 for (i in c(1:nrow(qecbnew))) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
341 qecbnew$Nb.Spirobranchus.lamarckii.total[[i]] <- ifelse(qecbnew$Nb.Spirobranchus.lamarckii.total[[i]] %in% c(NA, "NaN", "Inf", "-Inf"), sum(qecbnew[i, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B")], na.rm = TRUE) / sum(!is.na(qecbnew[i, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B")])) * 100, qecbnew$Nb.Spirobranchus.lamarckii.total[[i]])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
342 } # sum of only NAs/0 = NaN; so replace NaN by Na
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
343
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
344
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
345 for (i in c(1:nrow(qecbnew))) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
346 qecbnew$Nb.Spirobranchus.lamarckii.total[[i]] <- ifelse(qecbnew$Nb.Spirobranchus.lamarckii.total[[i]] == "NaN", NA, qecbnew$Nb.Spirobranchus.lamarckii.total[[i]])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
347 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
348
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
349 qecbnew$Nb.Spirobranchus.lamarckii.total <- as.integer(qecbnew$Nb.Spirobranchus.lamarckii.total)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
350
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
351 qecbnew$Nb.Spirobranchus.lamarckii.total.diff <- abs(qecbnew$Nb.Spirobranchus.lamarckii.total - qecbnew$Nb.Spirobranchus.lamarckii.total.ini)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
352 spirobranchus_diff <- qecbnew[, c("Nb.Spirobranchus.lamarckii.1B", "Nb.Spirobranchus.lamarckii.2B", "Nb.Spirobranchus.lamarckii.3B", "Nb.Spirobranchus.lamarckii.4B", "Nb.Spirobranchus.lamarckii.5B", "Nb.Spirobranchus.lamarckii.total", "Nb.Spirobranchus.lamarckii.total.ini", "mean.x.100", "Nb.Spirobranchus.lamarckii.total.diff")]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
353 spirobranchus_diff <- dplyr::arrange(spirobranchus_diff, desc(Nb.Spirobranchus.lamarckii.total.diff), mean.x.100)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
354 spirobranchus_diff <- dplyr::arrange(dplyr::filter(spirobranchus_diff, Nb.Spirobranchus.lamarckii.total.diff != 0 & mean.x.100 != 0), desc(Nb.Spirobranchus.lamarckii.total.diff))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
355
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
356 qecbnew <- subset(qecbnew, select = -c(Nb.Spirobranchus.lamarckii.total.ini, mean.x.100, Nb.Spirobranchus.lamarckii.total.diff))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
357
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
358 rm(qecbnew_spirobranchus, spirobranchus, spirobranchus_data, spirobranchus_diff)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
359
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
360 # do the same for spirorbis
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
361
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
362 qecbnew$Nb.spirorbis.total.ini <- qecbnew$Nb.spirorbis.total
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
363 qecbnew$Nb.spirorbis.total <- as.character(qecbnew$Nb.spirorbis.total)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
364
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
365 qecbnew_spirorbis <- (dplyr::filter(qecbnew, Nb.spirorbis.total %in% c(NA, "NaN", "Inf", "-Inf")))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
366 qecbnew_spirorbis[, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A")] <- sapply(qecbnew_spirorbis[, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A")], as.character)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
367 (spirobranchus_data <- subset(qecbnew_spirorbis, !is.na(qecbnew_spirorbis$Nb.spirorbis.1A) || !is.na(qecbnew_spirorbis$Nb.spirorbis.2A) || !is.na(qecbnew_spirorbis$Nb.spirorbis.3A) || !is.na(qecbnew_spirorbis$Nb.spirorbis.4A) || !is.na(qecbnew_spirorbis$Nb.spirorbis.5A))[, c("site_year_month_day", "Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A", "Nb.spirorbis.total")])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
368
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
369 # In contrast to Spirobranchus data, no encoding issues for spirorbis data, cfr when sub-quadrat 1A-5A are ALL encoded, NA for total.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
370
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
371 # some more issues however with "x200"count data
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
372
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
373 spirorbis <- subset(qecbnew, !is.na(qecbnew$Nb.spirorbis.1A) & !is.na(qecbnew$Nb.spirorbis.2A) & !is.na(qecbnew$Nb.spirorbis.3A) & !is.na(qecbnew$Nb.spirorbis.4A) & !is.na(qecbnew$Nb.spirorbis.5A) & !is.na(qecbnew$Nb.spirorbis.total))[, c("site_year_month_day", "Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A", "Nb.spirorbis.total")]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
374 for (i in c(1:nrow(spirorbis))) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
375 spirorbis$mean.x.200[[i]] <- sum(spirorbis[i, c(2:6)], na.rm = TRUE) / sum(!is.na(spirorbis[i, c(2:6)])) * 200
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
376 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
377 spirorbis$mean.x.200 <- unlist(spirorbis$mean.x.200)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
378 spirorbis$Nb.spirorbis.total <- as.numeric(spirorbis$Nb.spirorbis.total)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
379 for (i in c(1:nrow(spirorbis))) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
380 spirorbis$diff[[i]] <- spirorbis[i, "Nb.spirorbis.total"] - spirorbis[i, "mean.x.200"]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
381 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
382 spirorbis$diff <- abs(as.integer(spirorbis$diff))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
383 spirorbis <- dplyr::arrange(spirorbis, desc(diff), mean.x.200)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
384 (gonb_ilotstmichel_2015_04_18 <- dplyr::filter(spirorbis, site_year_month_day == "GONB_IlotStMichel.2015.04.18"))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
385 rm(gonb_ilotstmichel_2015_04_18)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
386 spirorbis <- dplyr::arrange(dplyr::filter(spirorbis, diff != 0 & mean.x.200 != 0), desc(diff))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
387
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
388 # check it all in the qecbnew df
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
389
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
390 for (i in c(1:nrow(qecbnew))) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
391 qecbnew$mean.x.200[[i]] <- sum(qecbnew[i, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A")], na.rm = TRUE) / sum(!is.na(qecbnew[i, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A")])) * 200
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
392 } # sum of only NAs/0 = NaN; so replace NaN by Na
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
393 qecbnew$mean.x.200 <- as.character(qecbnew$mean.x.200)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
394
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
395 for (i in c(1:nrow(qecbnew))) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
396 qecbnew$mean.x.200[[i]] <- ifelse(qecbnew$mean.x.200[[i]] == "NaN", NA, qecbnew$mean.x.200[[i]])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
397 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
398
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
399 qecbnew$mean.x.200 <- as.integer(qecbnew$mean.x.200)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
400
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
401 qecbnew$Nb.spirorbis.total <- as.integer(qecbnew$Nb.spirorbis.total)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
402 qecbnew$Nb.spirorbis.total.diff <- abs((qecbnew$Nb.spirorbis.total - qecbnew$mean.x.200))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
403 spirorbis_diff <- qecbnew[, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A", "Nb.spirorbis.total", "Nb.spirorbis.total.ini", "mean.x.200", "Nb.spirorbis.total.diff")]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
404 spirorbis_diff <- dplyr::arrange(spirorbis_diff, desc(Nb.spirorbis.total.diff), mean.x.200)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
405 spirorbis_diff <- dplyr::arrange(dplyr::filter(spirorbis_diff, Nb.spirorbis.total.diff != 0 & mean.x.200 != 0), desc(Nb.spirorbis.total.diff))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
406
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
407 qecbnew$Nb.spirorbis.total <- ifelse(qecbnew$Nb.spirorbis.total.diff != 0 & qecbnew$mean.x.200 != 0, qecbnew$mean.x.200, qecbnew$Nb.spirorbis.total)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
408 spirorbis_diff <- qecbnew[, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A", "Nb.spirorbis.total", "Nb.spirorbis.total.ini", "mean.x.200", "Nb.spirorbis.total.diff")]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
409 spirorbis_diff$Nb.spirorbis.total.diff <- abs(as.integer(spirorbis_diff$Nb.spirorbis.total.diff))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
410 spirorbis_diff <- dplyr::arrange(spirorbis_diff, desc(Nb.spirorbis.total.diff), mean.x.200)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
411 spirorbis_diff <- dplyr::arrange(dplyr::filter(spirorbis_diff, Nb.spirorbis.total.diff != 0 & mean.x.200 != 0), desc(Nb.spirorbis.total.diff))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
412 # ok, change made when data x 200 was not correct.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
413
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
414 # finally, change NA by mean.x200 for spirorbis total
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
415 qecbnew$Nb.spirorbis.total <- as.character(qecbnew$Nb.spirorbis.total)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
416 for (i in c(1:nrow(qecbnew))) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
417 qecbnew$Nb.spirorbis.total[[i]] <- ifelse(qecbnew$Nb.spirorbis.total[[i]] %in% c(NA, "NaN", "Inf", "-Inf"), sum(qecbnew[i, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A")], na.rm = TRUE) / sum(!is.na(qecbnew[i, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A")])) * 200, qecbnew$Nb.spirorbis.total[[i]])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
418 } # sum of only NAs/0 = NaN; so replace NaN by Na
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
419
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
420 for (i in c(1:nrow(qecbnew))) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
421 qecbnew$Nb.spirorbis.total[[i]] <- ifelse(qecbnew$Nb.spirorbis.total[[i]] == "NaN", NA, qecbnew$Nb.spirorbis.total[[i]])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
422 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
423
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
424 qecbnew$Nb.spirorbis.total <- as.integer(qecbnew$Nb.spirorbis.total)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
425
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
426 qecbnew$Nb.spirorbis.total.diff <- abs(qecbnew$Nb.spirorbis.total - qecbnew$Nb.spirorbis.total.ini)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
427 spirorbis_diff <- qecbnew[, c("Nb.spirorbis.1A", "Nb.spirorbis.2A", "Nb.spirorbis.3A", "Nb.spirorbis.4A", "Nb.spirorbis.5A", "Nb.spirorbis.total", "Nb.spirorbis.total.ini", "mean.x.200", "Nb.spirorbis.total.diff")]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
428 spirorbis_diff <- dplyr::arrange(spirorbis_diff, desc(Nb.spirorbis.total.diff), mean.x.200)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
429 spirorbis_diff <- dplyr::arrange(dplyr::filter(spirorbis_diff, Nb.spirorbis.total.diff != 0 & mean.x.200 != 0), desc(Nb.spirorbis.total.diff))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
430
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
431 qecbnew <- subset(qecbnew, select = -c(Nb.spirorbis.total.ini, mean.x.200, Nb.spirorbis.total.diff))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
432
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
433 rm(qecbnew_spirorbis, spirorbis, spirobranchus_data, spirorbis_diff, i)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
434
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
435
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
436 # dplyr::filter for abnormal data, based on histogram distribution of data
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
437
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
438 dplyr::filter(qecbnew, X..algues.brunes > 100)[, c("Site", "date_fiche", "Type.Bloc", "Numéro.Bloc.échantillon", "Face", "X..algues.brunes")]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
439 qecbnew$X..algues.brunes <- ifelse(qecbnew$X..algues.brunes > 100, 100, qecbnew$X..algues.brunes)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
440 dplyr::filter(qecbnew, X..algues.rouges > 100)[, c("Site", "date_fiche", "Type.Bloc", "Numéro.Bloc.échantillon", "Face", "X..algues.rouges")]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
441 qecbnew$X..algues.rouges <- ifelse(qecbnew$X..algues.rouges > 100, 100, qecbnew$X..algues.rouges)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
442
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
443
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
444 ## SCRIPT I - NAs <- 0 ; cfr previous comment makes no sense to have NA encoded when the presence of an organism is in reality = 0
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
445
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
446 # We are facing an issues with NA observations, because either they were not measured/counted, then they are effectively NAs; or these NAs = indeed "0"; but I cannot have NAs for variables that are included in the index determination, cfr if 5+0 = 5, 5+NA = NA; see for example site_year_month_day == "ARMO_Bilfot.2014.04.28", Nb.Spirobranchus.lamarckii.total is NA ...
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
447 # I theregore change these NAs by 0
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
448
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
449 # replace NAs by "0" for variables used in qecb determination
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
450 qecbnew[, c("X..algues.brunes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
451 "X..algues.rouges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
452 "X..Lithophyllum",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
453 "X..Cladophora",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
454 "Nb.Littorina.obtusata",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
455 "Nb.Gibbula.cineraria",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
456 "Nb.Gibbula.pennanti",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
457 "Nb.Gibbula.umbilicalis",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
458 "X..Eponges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
459 "X..Ascidies.Coloniales",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
460 "X..Ascidies.Solitaires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
461 "X..Bryozoaires.Dresses",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
462 "X..algues.vertes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
463 "X..Roche.Nue",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
464 "Nb.spirorbis.total",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
465 "X..Balanes.Vivantes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
466 "Nb.Spirobranchus.lamarckii.total",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
467 "X..Surface.Accolement")] <- lapply(qecbnew[,
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
468 c("X..algues.brunes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
469 "X..algues.rouges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
470 "X..Lithophyllum",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
471 "X..Cladophora",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
472 "Nb.Littorina.obtusata",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
473 "Nb.Gibbula.cineraria",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
474 "Nb.Gibbula.pennanti",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
475 "Nb.Gibbula.umbilicalis",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
476 "X..Eponges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
477 "X..Ascidies.Coloniales",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
478 "X..Ascidies.Solitaires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
479 "X..Bryozoaires.Dresses",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
480 "X..algues.vertes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
481 "X..Roche.Nue",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
482 "Nb.spirorbis.total",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
483 "X..Balanes.Vivantes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
484 "Nb.Spirobranchus.lamarckii.total",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
485 "X..Surface.Accolement")],
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
486 function(x) replace(x, is.na(x), 0))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
487
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
488 # and also replace NA for bivalve by 0 for EGMP and BASQ surveys cfr for accollement correction later on.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
489
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
490 qecbnew$X..Mytilus.sp. <- ifelse((substr(qecbnew$Site, 1, 4) %in% c("EGMP", "BASQ")) & is.na(qecbnew$X..Mytilus.sp.), 0, qecbnew$X..Mytilus.sp.)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
491 qecbnew$Nb.Crassostrea.gigas <- ifelse((substr(qecbnew$Site, 1, 4) %in% c("EGMP", "BASQ")) & is.na(qecbnew$Nb.Crassostrea.gigas), 0, qecbnew$Nb.Crassostrea.gigas)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
492 qecbnew$Nb.Ostrea.edulis <- ifelse((substr(qecbnew$Site, 1, 4) %in% c("EGMP", "BASQ")) & is.na(qecbnew$Nb.Ostrea.edulis), 0, qecbnew$Nb.Ostrea.edulis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
493
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
494
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
495 # add a region variable
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
496 region <- rep(NA, nrow(qecbnew))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
497 qecbnew <- tibble::add_column(qecbnew, region, .after = "Site_bis")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
498 qecbnew$region <- ifelse(qecbnew$Site %in% c("EGMP_GroinCou", "EGMP_PasEmsembert", "EGMP_BreeBains", "EGMP_PerreAntiochat", "EGMP_Chassiron", "BASQ_FlotsBleusZP", "BASQ_FlotsBleusZF"), "EGMP.BASQ", "Bretagne")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
499 rm(region)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
500 qecbnew <- dplyr::arrange(qecbnew, region, site_year_month_day, Type.Bloc, Numéro.Bloc.échantillon, Face)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
501
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
502 # accolement function according to recent 'retournement'
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
503
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
504 ## before I go further ahead, I have to correct for surface d'accollement for several variable for BM.FI !!
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
505
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
506 # not the same file name between script qecb script (qecbNew) and this script (qecbNew); doesn't matter, only appears here in the first dplyr::filter lines.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
507
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
508 qecbnew <- tibble::add_column(qecbnew, terri_ = substr(qecbnew$Site, 1, 4), .after = "Site_bis")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
509
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
510 qecbnew$X..Eponges_ini <- qecbnew$X..Eponges
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
511 qecbnew$X..Ascidies.Coloniales_ini <- qecbnew$X..Ascidies.Coloniales
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
512 qecbnew$X..Ascidies.Solitaires_ini <- qecbnew$X..Ascidies.Solitaires
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
513 qecbnew$X..Bryozoaires.Dresses_ini <- qecbnew$X..Bryozoaires.Dresses
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
514 qecbnew$X..Lithophyllum_ini <- qecbnew$X..Lithophyllum
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
515 qecbnew$X..Balanes.Vivantes_ini <- qecbnew$X..Balanes.Vivantes
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
516
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
517 df_bm_fs <- qecbnew %>% dplyr::filter(Type.Bloc == "Bloc mobile" & Face == "face supérieure")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
518 df_bm_fi <- qecbnew %>% dplyr::filter(Type.Bloc == "Bloc mobile" & Face == "face inférieure")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
519 df_bf <- qecbnew %>% dplyr::filter(Type.Bloc != "Bloc mobile")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
520
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
521 `%notin%` <- Negate(`%in%`)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
522
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
523 acco_fct <- function(var_) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
524
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
525 df_bm_fi$var_cor.acco. <<- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
526
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
527 for (i in c(1:nrow(df_bm_fi))) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
528
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
529 df_bm_fi$var_cor.acco.[[i]] <<- if (df_bm_fi$terri_[[i]] %notin% c("EGMP", "BASQ")) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
530 ifelse(#df_$Couleur.dominante %in% c("Rouge", "Brune", "Brune-Rouge") ||
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
531 df_bm_fs$Couleur.dominante[[i]] %in% c("Blanche", "Verte", "Blanche-Verte", "Colorée"), df_bm_fi[i, var_] / (100 - df_bm_fi$X..Surface.Accolement[[i]]) * 100, df_bm_fi[i, var_])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
532 } else {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
533 ifelse(df_bm_fs$Couleur.dominante[[i]] %in% c("Blanche", "Verte", "Blanche-Verte", "Colorée")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
534 & df_bm_fi$X..Surface.Accolement[[i]] != 0 # I have to use it in dplyr::filter this time as well for EGMP- BASQ (but not for Bretagne, although could be added, same result); identical/repeated measure for BM.FI and BM.FS
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
535 & df_bm_fs$X..Mytilus.sp.[[i]] == 0, df_bm_fi[i, var_] / (100 - df_bm_fi$X..Surface.Accolement[[i]]) * 100, df_bm_fi[i, var_])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
536 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
537
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
538 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
539
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
540 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
541
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
542 # I would only consider colors in c("Rouge", "Brune", "Brune-Rouge") for BM.FI correction [ and not the series c("Blanche-Brune", "Rouge", "Brune", "Blanche-Rouge", "Brune-Rouge", "Rouge-Verte", "Brune-Verte") ] ; and for BM.FS, the list c("Blanche", "Verte", "Colorée") => we do the correction for BM.FI accollement based on BM.FS color !!!
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
543
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
544
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
545 # apply acco_fct to BM.FI variables
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
546
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
547 apply_acco_fct <- function(var_) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
548
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
549 show(sort(df_bm_fi[, var_], decreasing = TRUE, index.return = FALSE)[1:50])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
550 pre_ <- as.vector(df_bm_fi[, var_])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
551 acco_fct(var_)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
552 df_bm_fi <<- tibble::add_column(df_bm_fi, var_cor. = df_bm_fi$var_cor.acco., .after = var_)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
553 show(sort(df_bm_fi$var_cor., decreasing = TRUE, index.return = FALSE)[1:50])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
554 df_bm_fi$var_cor. <<- as.numeric(ifelse(as.character(df_bm_fi$var_cor.) %in% c(NA, "NaN", "-Inf", "Inf"), "0", as.character(df_bm_fi$var_cor.)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
555 df_bm_fi$var_cor. <<- ifelse(df_bm_fi$var_cor. > 100, 100, df_bm_fi$var_cor.)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
556 show(sort(df_bm_fi$var_cor., decreasing = TRUE, index.return = FALSE)[1:50])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
557 show(length(na.omit(which(abs(as.vector(df_bm_fi$var_cor.) - pre_) != 0))) / na.omit(length(df_bm_fi$var_cor.)) * 100)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
558 par(mfrow = c(1, 3))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
559 hist(pre_, main = var_, xlab = "pre-corection")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
560 hist(df_bm_fi$var_cor., main = var_, xlab = "post-corection")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
561 hist(df_bm_fi[as.vector(which(abs(as.vector(df_bm_fi$var_cor.) - pre_) != 0)), var_], main = var_, xlab = "diff. post-pre != 0")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
562 par(mfrow = c(1, 1))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
563 df_bm_fi <<- df_bm_fi[, -which(names(df_bm_fi) %in% c(var_, "var_cor.acco."))]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
564 colnames(df_bm_fi)[colnames(df_bm_fi) == "var_cor."] <<- var_
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
565
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
566 rm(pre_)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
567
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
568 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
569
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
570 apply_acco_fct("X..Eponges")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
571 apply_acco_fct("X..Ascidies.Coloniales")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
572 apply_acco_fct("X..Ascidies.Solitaires")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
573 apply_acco_fct("X..Bryozoaires.Dresses")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
574 apply_acco_fct("X..Lithophyllum")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
575 apply_acco_fct("X..Balanes.Vivantes")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
576
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
577 qecbnew <- dplyr::bind_rows(df_bm_fs, df_bm_fi)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
578 qecbnew <- dplyr::bind_rows(qecbnew, df_bf)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
579
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
580 qecbnew <- dplyr::arrange(qecbnew, region, site_year_month_day, Type.Bloc, Numéro.Bloc.échantillon, Face)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
581
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
582 # do remove some more data ...
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
583 # "FINS_Quemenes.2020.10.16", bad encoding, I let know Anna Capietto to make changes => was corrected normally, so unactivate next time I download ESTAMP data
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
584 qecbnew <- dplyr::filter(qecbnew, site_year_month_day != "FINS_Quemenes.2020.10.16")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
585
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
586 # save the final qecbnew df_
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
587
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
588 qecb <- qecbnew
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
589
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
590
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
591 `%notin%` <- Negate(`%in%`)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
592
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
593 ## reorder and/or create new variables
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
594
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
595 # variable site_year_month_day moved for clarity purpose, not needed necessarily
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
596 qecb <- tibble::add_column(qecb, qecb$site_year_month_day, .after = "Site_bis")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
597 qecb <- qecb[, -which(names(qecb) %in% c("site_year_month_day"))]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
598 qecb <- dplyr::rename(qecb, site_year_month_day = `qecb$site_year_month_day`)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
599
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
600 # new variable period (nothing to see with the existing périod variable)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
601 period <- rep(NA, nrow(qecb))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
602 qecb <- tibble::add_column(qecb, period, .after = "Day")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
603 qecb$period <- ifelse(as.numeric(qecb$Month) < 7, "p1", "p2")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
604 qecb$period <- as.factor(qecb$period)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
605 rm(period)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
606
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
607 qecb <- dplyr::arrange(qecb, region, site_year_month_day, Type.Bloc, Numéro.Bloc.échantillon, Face)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
608
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
609 # NB: les infos surface d'accolement sont dupliquées de la face inf vers la face sup de blocs mobiles (même si peu de sens d'avoir cette info pour les face sup ...)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
610 # NB: les data "Abondance ressources ciblées par pêcheurs à pied" présentes uniquement pour les blocs mobiles sont dupliquées entre face inf et face sup.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
611
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
612 ## SCRIPT I - NAs <- 0
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
613
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
614 # already performed for part in the CB_qecb script ; but here I also consider mobile organisms, logical observation (or not) according to boulders, faces etc ... so more complete. Could be some kind of script fusion to only keep Na to 0 correction in one script, i.e. moving this script to the CB_qecb script ...
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
615
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
616 bretagne_bm <- dplyr::filter(qecb, region == "Bretagne" & Type.Bloc == "Bloc mobile")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
617 bretagne_bf <- dplyr::filter(qecb, region == "Bretagne" & Type.Bloc %in% c("Bloc fixé", "Roche en place"))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
618 egmp_basq_bm <- dplyr::filter(qecb, region == "EGMP.BASQ" & Type.Bloc == "Bloc mobile")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
619 egmp_basq_bf <- dplyr::filter(qecb, region == "EGMP.BASQ" & Type.Bloc %in% c("Bloc fixé", "Roche en place"))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
620
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
621 # replace NAs by "0" for variables used in qecb determination
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
622
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
623 bretagne_bm[, c(
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
624 "X..algues.brunes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
625 "Strate.algues.brunes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
626 "X..algues.rouges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
627 "Strate.algues.rouges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
628 "X..algues.vertes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
629 "Strate.algues.vertes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
630 "X..Cladophora",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
631 "X..Lithophyllum",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
632 "X..Recouvrement.Sediment", # is NA, then replace by 0 as well because no sense to have a NA value for "% recouvrement sédiment" as well.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
633 #"Type.Sediment",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
634 "X..Roche.Nue", # is NA, then replace by 0 as well because no sense to have a NA value for "% roche nue" as well.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
635 "Nb.Littorina.obtusata",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
636 "Nb.Gibbula.cineraria",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
637 "Nb.Gibbula.pennanti",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
638 "Nb.Gibbula.umbilicalis",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
639 "Nb.Phallusia.mamillata",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
640 "Nb.Tethya.aurantium",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
641 #"Nb.Spirobranchus.lamarckii.1B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
642 #"Nb.Spirobranchus.lamarckii.2B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
643 #"Nb.Spirobranchus.lamarckii.3B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
644 #"Nb.Spirobranchus.lamarckii.4B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
645 #"Nb.Spirobranchus.lamarckii.5B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
646 "Nb.Spirobranchus.lamarckii.total",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
647 #"Nb.spirorbis.1A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
648 #"Nb.spirorbis.2A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
649 #"Nb.spirorbis.3A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
650 #"Nb.spirorbis.4A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
651 #"Nb.spirorbis.5A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
652 "Nb.spirorbis.total",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
653 #.."Nb.Crassostrea.gigas",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
654 #.."Nb.Ostrea.edulis",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
655 #.."X..Mytilus.sp.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
656 #.."X..Hermelles",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
657 #.."X..Hydraires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
658 "X..Eponges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
659 "X..Ascidies.Coloniales",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
660 "X..Ascidies.Solitaires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
661 "X..Bryozoaires.Dresses",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
662 "X..Balanes.Vivantes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
663 #"Commentaires.Avant",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
664 "X..Surface.Accolement", # is NA, then replace by 0 as well because no sense to have a NA value for "% surface accolement" as well.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
665 #"Type.sustrat.observé",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
666 #"Commentaires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
667 "Nb.Cancer.pagurus..Tourteau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
668 "Nb.Necora.puber..Etrille.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
669 "Nb.Carcinus.maenas..Crabe.vert.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
670 "Nb.Nucella.lapilus..Pourpre.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
671 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
672 #.."Nb.Octopus.vulgaris..Poulpe.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
673 "Nb.Galathea..Galathées.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
674 #.."Nb.Paracentrotus.lividus..Oursin.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
675 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
676 "Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
677 "Nb.Haliotis.tuberculata..Ormeau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
678 #"Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
679 "Nb.Littorina.littorea..Bigorneau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
680 "Nb.Xantho.pilipes..Xanthe.poilu.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
681 "Nb.Mimachlamys.varia..Pétoncle.noir."
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
682 )
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
683 ] <- lapply(bretagne_bm[, c(
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
684 "X..algues.brunes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
685 "Strate.algues.brunes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
686 "X..algues.rouges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
687 "Strate.algues.rouges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
688 "X..algues.vertes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
689 "Strate.algues.vertes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
690 "X..Cladophora",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
691 "X..Lithophyllum",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
692 "X..Recouvrement.Sediment", # is NA, then replace by 0 as well because no sense to have a NA value for "% recouvrement sédiment" as well.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
693 #"Type.Sediment",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
694 "X..Roche.Nue", # is NA, then replace by 0 as well because no sense to have a NA value for "% roche nue" as well.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
695 "Nb.Littorina.obtusata",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
696 "Nb.Gibbula.cineraria",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
697 "Nb.Gibbula.pennanti",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
698 "Nb.Gibbula.umbilicalis",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
699 "Nb.Phallusia.mamillata",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
700 "Nb.Tethya.aurantium",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
701 #"Nb.Spirobranchus.lamarckii.1B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
702 #"Nb.Spirobranchus.lamarckii.2B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
703 #"Nb.Spirobranchus.lamarckii.3B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
704 #"Nb.Spirobranchus.lamarckii.4B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
705 #"Nb.Spirobranchus.lamarckii.5B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
706 "Nb.Spirobranchus.lamarckii.total",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
707 #"Nb.spirorbis.1A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
708 #"Nb.spirorbis.2A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
709 #"Nb.spirorbis.3A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
710 #"Nb.spirorbis.4A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
711 #"Nb.spirorbis.5A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
712 "Nb.spirorbis.total",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
713 #.."Nb.Crassostrea.gigas",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
714 #.."Nb.Ostrea.edulis",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
715 #.."X..Mytilus.sp.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
716 #.."X..Hermelles",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
717 #.."X..Hydraires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
718 "X..Eponges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
719 "X..Ascidies.Coloniales",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
720 "X..Ascidies.Solitaires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
721 "X..Bryozoaires.Dresses",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
722 "X..Balanes.Vivantes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
723 #"Commentaires.Avant",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
724 "X..Surface.Accolement", # is NA, then replace by 0 as well because no sense to have a NA value for "% surface accolement" as well.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
725 #"Type.sustrat.observé",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
726 #"Commentaires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
727 "Nb.Cancer.pagurus..Tourteau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
728 "Nb.Necora.puber..Etrille.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
729 "Nb.Carcinus.maenas..Crabe.vert.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
730 "Nb.Nucella.lapilus..Pourpre.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
731 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
732 #.."Nb.Octopus.vulgaris..Poulpe.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
733 "Nb.Galathea..Galathées.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
734 #.."Nb.Paracentrotus.lividus..Oursin.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
735 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
736 "Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
737 "Nb.Haliotis.tuberculata..Ormeau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
738 #"Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
739 "Nb.Littorina.littorea..Bigorneau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
740 "Nb.Xantho.pilipes..Xanthe.poilu.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
741 "Nb.Mimachlamys.varia..Pétoncle.noir."
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
742 )
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
743 ], function(x) replace(x, is.na(x), 0))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
744
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
745
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
746 # bretagne_bf
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
747 bretagne_bf[, c(
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
748 "X..algues.brunes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
749 "Strate.algues.brunes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
750 "X..algues.rouges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
751 "Strate.algues.rouges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
752 "X..algues.vertes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
753 "Strate.algues.vertes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
754 "X..Cladophora",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
755 "X..Lithophyllum",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
756 "X..Recouvrement.Sediment", # is NA, then replace by 0 as well because no sense to have a NA value for "% recouvrement sédiment" as well.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
757 #"Type.Sediment",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
758 "X..Roche.Nue", # is NA, then replace by 0 as well because no sense to have a NA value for "% roche nue" as well.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
759 "Nb.Littorina.obtusata",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
760 "Nb.Gibbula.cineraria",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
761 "Nb.Gibbula.pennanti",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
762 "Nb.Gibbula.umbilicalis",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
763 "Nb.Phallusia.mamillata",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
764 "Nb.Tethya.aurantium",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
765 #"Nb.Spirobranchus.lamarckii.1B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
766 #"Nb.Spirobranchus.lamarckii.2B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
767 #"Nb.Spirobranchus.lamarckii.3B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
768 #"Nb.Spirobranchus.lamarckii.4B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
769 #"Nb.Spirobranchus.lamarckii.5B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
770 "Nb.Spirobranchus.lamarckii.total",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
771 #"Nb.spirorbis.1A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
772 #"Nb.spirorbis.2A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
773 #"Nb.spirorbis.3A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
774 #"Nb.spirorbis.4A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
775 #"Nb.spirorbis.5A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
776 "Nb.spirorbis.total",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
777 #.."Nb.Crassostrea.gigas",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
778 #.."Nb.Ostrea.edulis",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
779 #.."X..Mytilus.sp.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
780 #.."X..Hermelles",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
781 #.."X..Hydraires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
782 "X..Eponges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
783 "X..Ascidies.Coloniales",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
784 "X..Ascidies.Solitaires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
785 "X..Bryozoaires.Dresses",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
786 "X..Balanes.Vivantes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
787 #"Commentaires.Avant",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
788 "X..Surface.Accolement"#, # is NA, then replace by 0 as well because no sense to have a NA value for "% surface accolement" as well.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
789 #"Type.sustrat.observé",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
790 #"Commentaires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
791 #."Nb.Cancer.pagurus..Tourteau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
792 #.."Nb.Necora.puber..Etrille.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
793 #."Nb.Carcinus.maenas..Crabe.vert.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
794 #."Nb.Nucella.lapilus..Pourpre.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
795 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
796 #.."Nb.Octopus.vulgaris..Poulpe.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
797 #."Nb.Galathea..Galathées.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
798 #.."Nb.Paracentrotus.lividus..Oursin.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
799 #."Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
800 #."Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
801 #."Nb.Haliotis.tuberculata..Ormeau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
802 #."Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
803 #."Nb.Littorina.littorea..Bigorneau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
804 #."Nb.Xantho.pilipes..Xanthe.poilu.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
805 #."Nb.Mimachlamys.varia..Pétoncle.noir."
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
806 )
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
807 ] <- lapply(bretagne_bf[, c(
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
808 "X..algues.brunes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
809 "Strate.algues.brunes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
810 "X..algues.rouges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
811 "Strate.algues.rouges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
812 "X..algues.vertes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
813 "Strate.algues.vertes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
814 "X..Cladophora",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
815 "X..Lithophyllum",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
816 "X..Recouvrement.Sediment", # is NA, then replace by 0 as well because no sense to have a NA value for "% recouvrement sédiment" as well.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
817 #"Type.Sediment",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
818 "X..Roche.Nue", # is NA, then replace by 0 as well because no sense to have a NA value for "% roche nue" as well.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
819 "Nb.Littorina.obtusata",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
820 "Nb.Gibbula.cineraria",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
821 "Nb.Gibbula.pennanti",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
822 "Nb.Gibbula.umbilicalis",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
823 "Nb.Phallusia.mamillata",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
824 "Nb.Tethya.aurantium",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
825 #"Nb.Spirobranchus.lamarckii.1B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
826 #"Nb.Spirobranchus.lamarckii.2B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
827 #"Nb.Spirobranchus.lamarckii.3B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
828 #"Nb.Spirobranchus.lamarckii.4B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
829 #"Nb.Spirobranchus.lamarckii.5B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
830 "Nb.Spirobranchus.lamarckii.total",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
831 #"Nb.spirorbis.1A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
832 #"Nb.spirorbis.2A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
833 #"Nb.spirorbis.3A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
834 #"Nb.spirorbis.4A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
835 #"Nb.spirorbis.5A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
836 "Nb.spirorbis.total",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
837 #.."Nb.Crassostrea.gigas",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
838 #.."Nb.Ostrea.edulis",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
839 #.."X..Mytilus.sp.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
840 #.."X..Hermelles",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
841 #.."X..Hydraires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
842 "X..Eponges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
843 "X..Ascidies.Coloniales",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
844 "X..Ascidies.Solitaires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
845 "X..Bryozoaires.Dresses",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
846 "X..Balanes.Vivantes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
847 #"Commentaires.Avant",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
848 "X..Surface.Accolement"#, # is NA, then replace by 0 as well because no sense to have a NA value for "% surface accolement" as well.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
849 #"Type.sustrat.observé",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
850 #"Commentaires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
851 #."Nb.Cancer.pagurus..Tourteau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
852 #.."Nb.Necora.puber..Etrille.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
853 #."Nb.Carcinus.maenas..Crabe.vert.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
854 #."Nb.Nucella.lapilus..Pourpre.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
855 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
856 #.."Nb.Octopus.vulgaris..Poulpe.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
857 #."Nb.Galathea..Galathées.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
858 #.."Nb.Paracentrotus.lividus..Oursin.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
859 #."Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
860 #."Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
861 #."Nb.Haliotis.tuberculata..Ormeau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
862 #."Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
863 #."Nb.Littorina.littorea..Bigorneau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
864 #."Nb.Xantho.pilipes..Xanthe.poilu.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
865 #."Nb.Mimachlamys.varia..Pétoncle.noir."
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
866 )
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
867 ], function(x) replace(x, is.na(x), 0))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
868
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
869
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
870 # egmp_basq_bm
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
871 egmp_basq_bm[, c(
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
872 "X..algues.brunes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
873 "Strate.algues.brunes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
874 "X..algues.rouges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
875 "Strate.algues.rouges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
876 "X..algues.vertes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
877 "Strate.algues.vertes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
878 "X..Cladophora",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
879 "X..Lithophyllum",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
880 "X..Recouvrement.Sediment", # is NA, then replace by 0 as well because no sense to have a NA value for "% recouvrement sédiment" as well.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
881 #"Type.Sediment",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
882 "X..Roche.Nue", # is NA, then replace by 0 as well because no sense to have a NA value for "% roche nue" as well.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
883 "Nb.Littorina.obtusata",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
884 "Nb.Gibbula.cineraria",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
885 "Nb.Gibbula.pennanti",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
886 "Nb.Gibbula.umbilicalis",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
887 "Nb.Phallusia.mamillata",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
888 "Nb.Tethya.aurantium",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
889 #"Nb.Spirobranchus.lamarckii.1B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
890 #"Nb.Spirobranchus.lamarckii.2B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
891 #"Nb.Spirobranchus.lamarckii.3B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
892 #"Nb.Spirobranchus.lamarckii.4B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
893 #"Nb.Spirobranchus.lamarckii.5B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
894 "Nb.Spirobranchus.lamarckii.total",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
895 #"Nb.spirorbis.1A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
896 #"Nb.spirorbis.2A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
897 #"Nb.spirorbis.3A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
898 #"Nb.spirorbis.4A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
899 #"Nb.spirorbis.5A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
900 "Nb.spirorbis.total",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
901 "Nb.Crassostrea.gigas",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
902 "Nb.Ostrea.edulis",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
903 "X..Mytilus.sp.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
904 "X..Hermelles",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
905 "X..Hydraires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
906 "X..Eponges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
907 "X..Ascidies.Coloniales",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
908 "X..Ascidies.Solitaires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
909 "X..Bryozoaires.Dresses",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
910 "X..Balanes.Vivantes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
911 #"Commentaires.Avant",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
912 "X..Surface.Accolement", # is NA, then replace by 0 as well because no sense to have a NA value for "% surface accolement" as well.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
913 #"Type.sustrat.observé",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
914 #"Commentaires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
915 "Nb.Cancer.pagurus..Tourteau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
916 "Nb.Necora.puber..Etrille.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
917 "Nb.Carcinus.maenas..Crabe.vert.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
918 "Nb.Nucella.lapilus..Pourpre.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
919 "Nb.Eriphia.verrucosa..Crabe.verruqueux.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
920 "Nb.Octopus.vulgaris..Poulpe.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
921 "Nb.Galathea..Galathées.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
922 "Nb.Paracentrotus.lividus..Oursin.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
923 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
924 "Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
925 "Nb.Haliotis.tuberculata..Ormeau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
926 "Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
927 "Nb.Littorina.littorea..Bigorneau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
928 "Nb.Xantho.pilipes..Xanthe.poilu.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
929 "Nb.Mimachlamys.varia..Pétoncle.noir."
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
930 )
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
931 ] <- lapply(egmp_basq_bm[, c(
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
932 "X..algues.brunes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
933 "Strate.algues.brunes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
934 "X..algues.rouges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
935 "Strate.algues.rouges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
936 "X..algues.vertes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
937 "Strate.algues.vertes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
938 "X..Cladophora",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
939 "X..Lithophyllum",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
940 "X..Recouvrement.Sediment", # is NA, then replace by 0 as well because no sense to have a NA value for "% recouvrement sédiment" as well.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
941 #"Type.Sediment",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
942 "X..Roche.Nue", # is NA, then replace by 0 as well because no sense to have a NA value for "% roche nue" as well.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
943 "Nb.Littorina.obtusata",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
944 "Nb.Gibbula.cineraria",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
945 "Nb.Gibbula.pennanti",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
946 "Nb.Gibbula.umbilicalis",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
947 "Nb.Phallusia.mamillata",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
948 "Nb.Tethya.aurantium",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
949 #"Nb.Spirobranchus.lamarckii.1B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
950 #"Nb.Spirobranchus.lamarckii.2B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
951 #"Nb.Spirobranchus.lamarckii.3B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
952 #"Nb.Spirobranchus.lamarckii.4B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
953 #"Nb.Spirobranchus.lamarckii.5B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
954 "Nb.Spirobranchus.lamarckii.total",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
955 #"Nb.spirorbis.1A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
956 #"Nb.spirorbis.2A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
957 #"Nb.spirorbis.3A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
958 #"Nb.spirorbis.4A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
959 #"Nb.spirorbis.5A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
960 "Nb.spirorbis.total",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
961 "Nb.Crassostrea.gigas",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
962 "Nb.Ostrea.edulis",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
963 "X..Mytilus.sp.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
964 "X..Hermelles",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
965 "X..Hydraires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
966 "X..Eponges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
967 "X..Ascidies.Coloniales",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
968 "X..Ascidies.Solitaires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
969 "X..Bryozoaires.Dresses",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
970 "X..Balanes.Vivantes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
971 #"Commentaires.Avant",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
972 "X..Surface.Accolement", # is NA, then replace by 0 as well because no sense to have a NA value for "% surface accolement" as well.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
973 #"Type.sustrat.observé",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
974 #"Commentaires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
975 "Nb.Cancer.pagurus..Tourteau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
976 "Nb.Necora.puber..Etrille.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
977 "Nb.Carcinus.maenas..Crabe.vert.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
978 "Nb.Nucella.lapilus..Pourpre.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
979 "Nb.Eriphia.verrucosa..Crabe.verruqueux.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
980 "Nb.Octopus.vulgaris..Poulpe.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
981 "Nb.Galathea..Galathées.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
982 "Nb.Paracentrotus.lividus..Oursin.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
983 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
984 "Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
985 "Nb.Haliotis.tuberculata..Ormeau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
986 "Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
987 "Nb.Littorina.littorea..Bigorneau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
988 "Nb.Xantho.pilipes..Xanthe.poilu.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
989 "Nb.Mimachlamys.varia..Pétoncle.noir."
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
990 )
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
991 ], function(x) replace(x, is.na(x), 0))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
992
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
993
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
994 # egmp_basq_bf
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
995 egmp_basq_bf[, c(
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
996 "X..algues.brunes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
997 "Strate.algues.brunes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
998 "X..algues.rouges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
999 "Strate.algues.rouges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1000 "X..algues.vertes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1001 "Strate.algues.vertes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1002 "X..Cladophora",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1003 "X..Lithophyllum",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1004 "X..Recouvrement.Sediment", # is NA, then replace by 0 as well because no sense to have a NA value for "% recouvrement sédiment" as well.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1005 #"Type.Sediment",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1006 "X..Roche.Nue", # is NA, then replace by 0 as well because no sense to have a NA value for "% roche nue" as well.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1007 "Nb.Littorina.obtusata",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1008 "Nb.Gibbula.cineraria",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1009 "Nb.Gibbula.pennanti",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1010 "Nb.Gibbula.umbilicalis",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1011 "Nb.Phallusia.mamillata",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1012 "Nb.Tethya.aurantium",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1013 #"Nb.Spirobranchus.lamarckii.1B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1014 #"Nb.Spirobranchus.lamarckii.2B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1015 #"Nb.Spirobranchus.lamarckii.3B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1016 #"Nb.Spirobranchus.lamarckii.4B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1017 #"Nb.Spirobranchus.lamarckii.5B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1018 "Nb.Spirobranchus.lamarckii.total",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1019 #"Nb.spirorbis.1A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1020 #"Nb.spirorbis.2A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1021 #"Nb.spirorbis.3A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1022 #"Nb.spirorbis.4A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1023 #"Nb.spirorbis.5A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1024 "Nb.spirorbis.total",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1025 "Nb.Crassostrea.gigas",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1026 "Nb.Ostrea.edulis",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1027 "X..Mytilus.sp.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1028 "X..Hermelles",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1029 "X..Hydraires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1030 "X..Eponges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1031 "X..Ascidies.Coloniales",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1032 "X..Ascidies.Solitaires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1033 "X..Bryozoaires.Dresses",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1034 "X..Balanes.Vivantes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1035 #"Commentaires.Avant",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1036 "X..Surface.Accolement"#, # is NA, then replace by 0 as well because no sense to have a NA value for "% surface accolement" as well.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1037 #"Type.sustrat.observé",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1038 #"Commentaires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1039 #."Nb.Cancer.pagurus..Tourteau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1040 #.."Nb.Necora.puber..Etrille.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1041 #."Nb.Carcinus.maenas..Crabe.vert.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1042 #."Nb.Nucella.lapilus..Pourpre.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1043 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1044 #.."Nb.Octopus.vulgaris..Poulpe.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1045 #."Nb.Galathea..Galathées.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1046 #.."Nb.Paracentrotus.lividus..Oursin.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1047 #."Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1048 #."Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1049 #."Nb.Haliotis.tuberculata..Ormeau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1050 #."Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1051 #."Nb.Littorina.littorea..Bigorneau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1052 #."Nb.Xantho.pilipes..Xanthe.poilu.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1053 #."Nb.Mimachlamys.varia..Pétoncle.noir."
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1054 )
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1055 ] <- lapply(egmp_basq_bf[, c(
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1056 "X..algues.brunes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1057 "Strate.algues.brunes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1058 "X..algues.rouges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1059 "Strate.algues.rouges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1060 "X..algues.vertes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1061 "Strate.algues.vertes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1062 "X..Cladophora",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1063 "X..Lithophyllum",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1064 "X..Recouvrement.Sediment", # is NA, then replace by 0 as well because no sense to have a NA value for "% recouvrement sédiment" as well.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1065 #"Type.Sediment",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1066 "X..Roche.Nue", # is NA, then replace by 0 as well because no sense to have a NA value for "% roche nue" as well.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1067 "Nb.Littorina.obtusata",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1068 "Nb.Gibbula.cineraria",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1069 "Nb.Gibbula.pennanti",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1070 "Nb.Gibbula.umbilicalis",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1071 "Nb.Phallusia.mamillata",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1072 "Nb.Tethya.aurantium",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1073 #"Nb.Spirobranchus.lamarckii.1B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1074 #"Nb.Spirobranchus.lamarckii.2B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1075 #"Nb.Spirobranchus.lamarckii.3B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1076 #"Nb.Spirobranchus.lamarckii.4B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1077 #"Nb.Spirobranchus.lamarckii.5B",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1078 "Nb.Spirobranchus.lamarckii.total",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1079 #"Nb.spirorbis.1A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1080 #"Nb.spirorbis.2A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1081 #"Nb.spirorbis.3A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1082 #"Nb.spirorbis.4A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1083 #"Nb.spirorbis.5A",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1084 "Nb.spirorbis.total",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1085 "Nb.Crassostrea.gigas",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1086 "Nb.Ostrea.edulis",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1087 "X..Mytilus.sp.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1088 "X..Hermelles",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1089 "X..Hydraires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1090 "X..Eponges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1091 "X..Ascidies.Coloniales",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1092 "X..Ascidies.Solitaires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1093 "X..Bryozoaires.Dresses",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1094 "X..Balanes.Vivantes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1095 #"Commentaires.Avant",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1096 "X..Surface.Accolement"#, # is NA, then replace by 0 as well because no sense to have a NA value for "% surface accolement" as well.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1097 #"Type.sustrat.observé",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1098 #"Commentaires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1099 #."Nb.Cancer.pagurus..Tourteau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1100 #.."Nb.Necora.puber..Etrille.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1101 #."Nb.Carcinus.maenas..Crabe.vert.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1102 #."Nb.Nucella.lapilus..Pourpre.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1103 #.."Nb.Eriphia.verrucosa..Crabe.verruqueux.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1104 #.."Nb.Octopus.vulgaris..Poulpe.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1105 #."Nb.Galathea..Galathées.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1106 #.."Nb.Paracentrotus.lividus..Oursin.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1107 #."Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1108 #."Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1109 #."Nb.Haliotis.tuberculata..Ormeau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1110 #."Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1111 #."Nb.Littorina.littorea..Bigorneau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1112 #."Nb.Xantho.pilipes..Xanthe.poilu.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1113 #."Nb.Mimachlamys.varia..Pétoncle.noir."
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1114 )
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1115 ], function(x) replace(x, is.na(x), 0))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1116
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1117
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1118 # merge dfs.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1119 qecbnato0 <- dplyr::bind_rows(bretagne_bm, bretagne_bf)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1120 qecbnato0 <- dplyr::bind_rows(qecbnato0, egmp_basq_bm)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1121 qecbnato0 <- dplyr::bind_rows(qecbnato0, egmp_basq_bf)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1122
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1123 qecbnato0 <- dplyr::arrange(qecbnato0, region, site_year_month_day, Type.Bloc, Numéro.Bloc.échantillon, Face)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1124
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1125 rm(bretagne_bm, bretagne_bf, egmp_basq_bm, egmp_basq_bf)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1126
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1127
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1128 ## analyse matricielle
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1129
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1130 # NB some variables were dplyr::renamed or created, cfr I originally merged qecb and ivr data in below script to do some correlation analysis. This is not the case anymore, so no more merging anymore.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1131
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1132 qecbnato0 <- tibble::add_column(qecbnato0, region.site_year_month_day = paste0(qecbnato0$region, qecbnato0$site_year_month_day), .before = "region")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1133
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1134
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1135 numero_quadrat <- stringr::str_sub(qecbnato0$quadrat_bis, start = -1)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1136 qecbnato0 <- tibble::add_column(qecbnato0, numero_quadrat, .after = "quadrat_bis")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1137 rm(numero_quadrat)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1138 qecbnato0$numero_quadrat <- as.integer(qecbnato0$numero_quadrat)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1139
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1140
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1141 qecbnato0$Year <- as.integer(qecbnato0$Year)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1142 qecbnato0$Month <- as.integer(qecbnato0$Month)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1143 qecbnato0$Day <- as.integer(qecbnato0$Day)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1144
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1145 ############################################################
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1146 #!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1147 # Anna still hasn't corrected for boulder nb in FINS_Quemenes.2020.10.16 data encoding ! removed from the df_
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1148 qecbnato0 <- qecbnato0 %>% dplyr::filter(site_year_month_day != "FINS_Quemenes.2020.10.16")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1149 ############################################################
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1150
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1151 # what to do with spirorbes & Nb.Spirobranchus.lamarckii.total? log10 transformation
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1152
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1153 qecbnato0 <- tibble::add_column(qecbnato0, log10.Nb.spirorbis.total = log10(qecbnato0$Nb.spirorbis.total + 1), .after = "Nb.spirorbis.total")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1154 qecbnato0 <- tibble::add_column(qecbnato0, log10.Nb.Spirobranchus.lamarckii.total = log10(qecbnato0$Nb.Spirobranchus.lamarckii.total + 1), .after = "Nb.Spirobranchus.lamarckii.total")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1155
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1156 saveRDS(qecbnato0, "qecbnato0.RDS")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1157
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1158
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1159 ###############################################################
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1160 # #
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1161 # Start dissimilarity calculation with some data handling #
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1162 # #
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1163 ###############################################################
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1164
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1165 # first, create vector (4) for qecb and fishing by region (same as above)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1166
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1167 bret_egmp_basq_qecb <- c(
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1168 "X..algues.brunes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1169 "X..algues.rouges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1170 "X..algues.vertes",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1171 "X..Cladophora",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1172 "X..Lithophyllum",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1173 "Nb.Littorina.obtusata",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1174 "Nb.Gibbula.cineraria",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1175 "Nb.Gibbula.pennanti",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1176 "Nb.Gibbula.umbilicalis",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1177 "Nb.Phallusia.mamillata",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1178 "Nb.Tethya.aurantium",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1179 "Nb.Spirobranchus.lamarckii.total",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1180 "Nb.spirorbis.total",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1181 "X..Eponges",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1182 "X..Ascidies.Coloniales",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1183 "X..Ascidies.Solitaires",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1184 "X..Bryozoaires.Dresses",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1185 "X..Balanes.Vivantes"
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1186 #, "X..Recouvrement.Sediment"
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1187 #, "X..Roche.Nue"
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1188 #, "X..Surface.Accolement"
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1189 )
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1190
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1191 egmp_basq_qecb <- c("Nb.Crassostrea.gigas", "Nb.Ostrea.edulis", "X..Mytilus.sp.", "X..Hermelles", "X..Hydraires")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1192
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1193 bret_egmp_basq_fishing <- c("Nb.Cancer.pagurus..Tourteau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1194 "Nb.Necora.puber..Etrille.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1195 "Nb.Carcinus.maenas..Crabe.vert.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1196 "Nb.Nucella.lapilus..Pourpre.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1197 "Nb.Galathea..Galathées.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1198 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1199 "Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1200 "Nb.Haliotis.tuberculata..Ormeau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1201 "Nb.Littorina.littorea..Bigorneau.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1202 "Nb.Xantho.pilipes..Xanthe.poilu.",
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1203 "Nb.Mimachlamys.varia..Pétoncle.noir.")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1204
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1205 egmp_basq_fishing <- c("Nb.Eriphia.verrucosa..Crabe.verruqueux.", "Nb.Octopus.vulgaris..Poulpe.", "Nb.Paracentrotus.lividus..Oursin.", "Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1206
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1207 # here I can choose to either replace spirorbis and/or spirobranchus by their log10 transformation in bret_egmp_basq_qecb vector
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1208 bret_egmp_basq_qecb <- replace(bret_egmp_basq_qecb, bret_egmp_basq_qecb == "Nb.spirorbis.total", "log10.Nb.spirorbis.total")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1209 saveRDS(bret_egmp_basq_qecb, "bret_egmp_basq_qecb.RDS")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1210
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1211
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1212 #############################################################
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1213 # #
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1214 # Compute dissimilarity #
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1215 # #
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1216 #############################################################
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1217 ### determination of coefficient of dissimilarity face sup mobile bloc vs fixed bloc
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1218
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1219 # loop in a fct
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1220
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1221 matri_fct_bmf <- function(data, conca) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1222
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1223 matri_df <- data
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1224
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1225 for (x in c(1:length(unique(matri_df$site_year_month_day)))) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1226
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1227 qecbnato0_x <- matri_df %>% dplyr::filter(site_year_month_day == unique(matri_df$site_year_month_day)[[x]])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1228
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1229 rownames(qecbnato0_x) <- paste0(qecbnato0_x$Type.Bloc, "_", qecbnato0_x$Face, "_", qecbnato0_x$Numéro.Bloc.échantillon, "_", qecbnato0_x$quadrat_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1230
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1231
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1232 mtxdis <- vegan::vegdist(
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1233 sqrt(qecbnato0_x[, conca]), #Transform your species abundance data_ Typically, raw abundances are transformed prior to analysis. Usually you will use square root, fourth-root, log(X+1), or presence-absence (square root being least extreme, P/A being most). I would start with square root. (https://stats.stackexchange.com/questions/234495/double-zeroes-problem-with-euclidean-distance-and-abundance-data-is-the-proble)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1234
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1235 na.rm = TRUE,
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1236 method = "bray" #Construct species abundance dissimilarity matrices with Bray-Curtis. If your data contains samples that are all-zero you will run into the double zero problem. This can be overcome by using a zero-adjusted Bray-Curtis coefficient, which is sometimes referred to as a 'dummy variable' which damps down the similarity fluctuations between samples that are both zero (undefined). => see below for zero-adjusted Bray-Curtis coefficient ; #another possibility, sqrt + 1 ??
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1237 )
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1238
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1239
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1240 #https://rdrr.io/github/phytomosaic/ecole/man/bray0.html
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1241 # mtxdis <- ecole::bray0(
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1242 # sqrt
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1243 # (qecbnato0_x[,conca]), na.rm = TRUE)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1244
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1245 expand.grid(mtxdis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1246
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1247 mtxdisdf_ <- as.data.frame(as.matrix(mtxdis))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1248
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1249 a_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1250 b_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1251 c_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1252 d_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1253 e_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1254 f_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1255 g_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1256 h_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1257 i_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1258 j_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1259 k_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1260 l_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1261 m_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1262 n_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1263
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1264 for (z in c(1:nrow(mtxdisdf_))) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1265
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1266 a_[[z]] <- (paste0(rownames(mtxdisdf_[z + 1, ]), " & ", ifelse(nrow(mtxdisdf_) >= 1, colnames(mtxdisdf_[1]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1267 b_[[z]] <- (paste0(rownames(mtxdisdf_[z + 2, ]), " & ", ifelse(nrow(mtxdisdf_) >= 2, colnames(mtxdisdf_[2]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1268 c_[[z]] <- (paste0(rownames(mtxdisdf_[z + 3, ]), " & ", ifelse(nrow(mtxdisdf_) >= 3, colnames(mtxdisdf_[3]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1269 d_[[z]] <- (paste0(rownames(mtxdisdf_[z + 4, ]), " & ", ifelse(nrow(mtxdisdf_) >= 4, colnames(mtxdisdf_[4]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1270 e_[[z]] <- (paste0(rownames(mtxdisdf_[z + 5, ]), " & ", ifelse(nrow(mtxdisdf_) >= 5, colnames(mtxdisdf_[5]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1271 f_[[z]] <- (paste0(rownames(mtxdisdf_[z + 6, ]), " & ", ifelse(nrow(mtxdisdf_) >= 6, colnames(mtxdisdf_[6]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1272 g_[[z]] <- (paste0(rownames(mtxdisdf_[z + 7, ]), " & ", ifelse(nrow(mtxdisdf_) >= 7, colnames(mtxdisdf_[7]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1273 h_[[z]] <- (paste0(rownames(mtxdisdf_[z + 8, ]), " & ", ifelse(nrow(mtxdisdf_) >= 8, colnames(mtxdisdf_[8]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1274 i_[[z]] <- (paste0(rownames(mtxdisdf_[z + 9, ]), " & ", ifelse(nrow(mtxdisdf_) >= 9, colnames(mtxdisdf_[9]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1275 j_[[z]] <- (paste0(rownames(mtxdisdf_[z + 10, ]), " & ", ifelse(nrow(mtxdisdf_) >= 10, colnames(mtxdisdf_[10]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1276 k_[[z]] <- (paste0(rownames(mtxdisdf_[z + 11, ]), " & ", ifelse(nrow(mtxdisdf_) >= 11, colnames(mtxdisdf_[11]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1277 l_[[z]] <- (paste0(rownames(mtxdisdf_[z + 12, ]), " & ", ifelse(nrow(mtxdisdf_) >= 12, colnames(mtxdisdf_[12]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1278 m_[[z]] <- (paste0(rownames(mtxdisdf_[z + 13, ]), " & ", ifelse(nrow(mtxdisdf_) >= 13, colnames(mtxdisdf_[13]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1279 n_[[z]] <- (paste0(rownames(mtxdisdf_[z + 14, ]), " & ", ifelse(nrow(mtxdisdf_) >= 14, colnames(mtxdisdf_[14]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1280
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1281 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1282
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1283 rm(z)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1284
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1285 y <- length(a_) - (ifelse(nrow(mtxdisdf_) >= 1, 1, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1286 a_ <- a_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1287 y <- length(b_) - (ifelse(nrow(mtxdisdf_) >= 2, 2, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1288 b_ <- b_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1289 y <- length(c_) - (ifelse(nrow(mtxdisdf_) >= 3, 3, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1290 c_ <- c_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1291 y <- length(d_) - (ifelse(nrow(mtxdisdf_) >= 4, 4, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1292 d_ <- d_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1293 y <- length(e_) - (ifelse(nrow(mtxdisdf_) >= 5, 5, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1294 e_ <- e_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1295 y <- length(f_) - (ifelse(nrow(mtxdisdf_) >= 6, 6, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1296 f_ <- f_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1297 y <- length(g_) - (ifelse(nrow(mtxdisdf_) >= 7, 7, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1298 g_ <- g_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1299 y <- length(h_) - (ifelse(nrow(mtxdisdf_) >= 8, 8, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1300 h_ <- h_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1301 y <- length(i_) - (ifelse(nrow(mtxdisdf_) >= 9, 9, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1302 i_ <- i_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1303 y <- length(j_) - (ifelse(nrow(mtxdisdf_) >= 10, 10, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1304 j_ <- j_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1305 y <- length(k_) - (ifelse(nrow(mtxdisdf_) >= 11, 11, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1306 k_ <- k_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1307 y <- length(l_) - (ifelse(nrow(mtxdisdf_) >= 12, 12, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1308 l_ <- l_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1309 y <- length(m_) - (ifelse(nrow(mtxdisdf_) >= 13, 13, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1310 m_ <- m_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1311 y <- length(n_) - (ifelse(nrow(mtxdisdf_) >= 14, 14, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1312 n_ <- n_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1313
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1314 rm(y)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1315
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1316 name_ <- c(a_, b_, c_, d_, e_, f_, g_, h_, i_, j_, k_, l_, m_, n_)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1317 df_ <- data.frame(expand.grid(mtxdis), name_[1:nrow(expand.grid(mtxdis))])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1318 names(df_) <- c("dist.", "name_")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1319
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1320 rm(a_, b_, c_, d_, e_, f_, g_, h_, i_, j_, k_, l_, m_, n_)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1321 rm(name_)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1322
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1323 q_ <- strsplit(df_$name_, " & ")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1324 mat_ <- matrix(unlist(q_), ncol = 2, byrow = TRUE)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1325 q_df_ <- as.data.frame(matrix(unlist(q_), ncol = 2, byrow = TRUE))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1326 df_ <- dplyr::bind_cols(df_, q_df_)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1327
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1328 rm(q_, mat_, q_df_)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1329
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1330 split_ <- strsplit(df_$V1, "_")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1331 v1_split_ <- as.data.frame(matrix(unlist(split_), ncol = 4, byrow = TRUE))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1332 split_ <- strsplit(df_$V2, "_")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1333 v2_split_ <- as.data.frame(matrix(unlist(split_), ncol = 4, byrow = TRUE))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1334
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1335 df_ <- dplyr::bind_cols(df_, v1_split_)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1336 df_ <- dplyr::bind_cols(df_, v2_split_)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1337 df_red_ <- subset(df_, V4...8 == V4...12 & V1...5 != V1...9)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1338 site_year_month_day <- rep(unique(qecbnato0_x$site_year_month_day), nrow(df_red_))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1339
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1340 df_red_ <- tibble::add_column(df_red_, site_year_month_day, .before = "dist.")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1341
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1342 rm(split_, v1_split_, v2_split_)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1343 rm(mtxdis, mtxdisdf_, df_, site_year_month_day)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1344
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1345 matri_list[[x]] <- df_red_
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1346 matri_list <<- matri_list
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1347
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1348 rm(df_red_, qecbnato0_x, x)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1349
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1350 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1351
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1352 matri_df <- do.call("rbind", matri_list)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1353
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1354 names(matri_df) <- c("site_year_month_day", "dist.", "name_", "name_left", "name_right", "Type.Bloc.left", "Face.left", "Numéro.Bloc.échantillon.left", "Quadrat.left", "Type.Bloc.right", "Face.right", "Numéro.Bloc.échantillon.right", "Quadrat.right")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1355
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1356 matri_df <<- matri_df
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1357
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1358 hist(matri_df$dist.)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1359
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1360 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1361
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1362 data_ <- dplyr::filter(qecbnato0, Face == "face supérieure")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1363 data_$Type.Bloc <- ifelse(as.character(data_$Type.Bloc) == "Roche en place", "Bloc fixé", as.character(data_$Type.Bloc))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1364 matri_list <- vector("list", length(unique(data_$site_year_month_day)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1365
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1366 matri_fct_bmf(data = data_, conca = c(bret_egmp_basq_qecb, egmp_basq_qecb))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1367 hist(matri_df$dist., main = c(paste("Histo. of Bray (0-adjusted) dist. dissimilarity measures"), paste(" (sqrt transfo) - BMfs vs BF -")))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1368
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1369 matri_full_bm_bf_fs <- matri_df
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1370
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1371
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1372 rm(data_, matri_df, matri_list)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1373
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1374
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1375 ### determination of coefficient of dissimilarity between blocs mobiles face sup vs face inf.
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1376
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1377 # loop in a fct
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1378
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1379 matri_fct_bmm <- function(data, conca) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1380
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1381 matri_df <- data
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1382
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1383 for (x in c(1:length(unique(matri_df$site_year_month_day)))) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1384
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1385 qecbnato0_x <- matri_df %>% dplyr::filter(site_year_month_day == unique(matri_df$site_year_month_day)[[x]])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1386
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1387 rownames(qecbnato0_x) <- paste0(qecbnato0_x$Type.Bloc, "_", qecbnato0_x$Face, "_", qecbnato0_x$Numéro.Bloc.échantillon, "_", qecbnato0_x$quadrat_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1388
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1389
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1390 mtxdis <- vegan::vegdist(
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1391 sqrt(qecbnato0_x[, c(bret_egmp_basq_qecb)]), #Transform your species abundance data_ Typically, raw abundances are transformed prior to analysis. Usually you will use square root, fourth-root, log(X+1), or presence-absence (square root being least extreme, P/A being most). I would start with square root. (https://stats.stackexchange.com/questions/234495/double-zeroes-problem-with-euclidean-distance-and-abundance-data-is-the-proble)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1392 na.rm = TRUE,
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1393 method = "bray" #Construct species abundance dissimilarity matrices with Bray-Curtis. If your data contains samples that are all-zero you will run into the double zero problem. This can be overcome by using a zero-adjusted Bray-Curtis coefficient, which is sometimes referred to as a 'dummy variable' which damps down the similarity fluctuations between samples that are both zero (undefined). => see below for zero-adjusted Bray-Curtis coefficient ; #another possibility, sqrt + 1 ??
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1394 )
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1395
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1396
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1397 #mtxdis <- ecole::bray0(
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1398 # sqrt(qecbnato0_x[, conca]), na.rm = TRUE)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1399
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1400
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1401 expand.grid(mtxdis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1402
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1403 mtxdisdf_ <- as.data.frame(as.matrix(mtxdis))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1404
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1405 a_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1406 b_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1407 c_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1408 d_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1409 e_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1410 f_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1411 g_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1412 h_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1413 i_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1414 j_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1415 k_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1416 l_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1417 m_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1418 n_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1419 o_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1420 p_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1421 q_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1422 r_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1423 s_ <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1424
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1425 for (z in c(1:nrow(mtxdisdf_))) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1426
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1427 a_[[z]] <- (paste0(rownames(mtxdisdf_[z + 1, ]), " & ", ifelse(nrow(mtxdisdf_) >= 1, colnames(mtxdisdf_[1]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1428 b_[[z]] <- (paste0(rownames(mtxdisdf_[z + 2, ]), " & ", ifelse(nrow(mtxdisdf_) >= 2, colnames(mtxdisdf_[2]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1429 c_[[z]] <- (paste0(rownames(mtxdisdf_[z + 3, ]), " & ", ifelse(nrow(mtxdisdf_) >= 3, colnames(mtxdisdf_[3]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1430 d_[[z]] <- (paste0(rownames(mtxdisdf_[z + 4, ]), " & ", ifelse(nrow(mtxdisdf_) >= 4, colnames(mtxdisdf_[4]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1431 e_[[z]] <- (paste0(rownames(mtxdisdf_[z + 5, ]), " & ", ifelse(nrow(mtxdisdf_) >= 5, colnames(mtxdisdf_[5]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1432 f_[[z]] <- (paste0(rownames(mtxdisdf_[z + 6, ]), " & ", ifelse(nrow(mtxdisdf_) >= 6, colnames(mtxdisdf_[6]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1433 g_[[z]] <- (paste0(rownames(mtxdisdf_[z + 7, ]), " & ", ifelse(nrow(mtxdisdf_) >= 7, colnames(mtxdisdf_[7]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1434 h_[[z]] <- (paste0(rownames(mtxdisdf_[z + 8, ]), " & ", ifelse(nrow(mtxdisdf_) >= 8, colnames(mtxdisdf_[8]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1435 i_[[z]] <- (paste0(rownames(mtxdisdf_[z + 9, ]), " & ", ifelse(nrow(mtxdisdf_) >= 9, colnames(mtxdisdf_[9]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1436 j_[[z]] <- (paste0(rownames(mtxdisdf_[z + 10, ]), " & ", ifelse(nrow(mtxdisdf_) >= 10, colnames(mtxdisdf_[10]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1437 k_[[z]] <- (paste0(rownames(mtxdisdf_[z + 11, ]), " & ", ifelse(nrow(mtxdisdf_) >= 11, colnames(mtxdisdf_[11]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1438 l_[[z]] <- (paste0(rownames(mtxdisdf_[z + 12, ]), " & ", ifelse(nrow(mtxdisdf_) >= 12, colnames(mtxdisdf_[12]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1439 m_[[z]] <- (paste0(rownames(mtxdisdf_[z + 13, ]), " & ", ifelse(nrow(mtxdisdf_) >= 13, colnames(mtxdisdf_[13]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1440 n_[[z]] <- (paste0(rownames(mtxdisdf_[z + 14, ]), " & ", ifelse(nrow(mtxdisdf_) >= 14, colnames(mtxdisdf_[14]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1441 o_[[z]] <- (paste0(rownames(mtxdisdf_[z + 15, ]), " & ", ifelse(nrow(mtxdisdf_) >= 15, colnames(mtxdisdf_[15]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1442 p_[[z]] <- (paste0(rownames(mtxdisdf_[z + 16, ]), " & ", ifelse(nrow(mtxdisdf_) >= 16, colnames(mtxdisdf_[16]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1443 q_[[z]] <- (paste0(rownames(mtxdisdf_[z + 17, ]), " & ", ifelse(nrow(mtxdisdf_) >= 17, colnames(mtxdisdf_[17]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1444 r_[[z]] <- (paste0(rownames(mtxdisdf_[z + 18, ]), " & ", ifelse(nrow(mtxdisdf_) >= 18, colnames(mtxdisdf_[18]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1445 s_[[z]] <- (paste0(rownames(mtxdisdf_[z + 19, ]), " & ", ifelse(nrow(mtxdisdf_) >= 19, colnames(mtxdisdf_[19]), NA)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1446
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1447 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1448
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1449 rm(z)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1450
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1451 y <- length(a_) - (ifelse(nrow(mtxdisdf_) >= 1, 1, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1452 a_ <- a_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1453 y <- length(b_) - (ifelse(nrow(mtxdisdf_) >= 2, 2, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1454 b_ <- b_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1455 y <- length(c_) - (ifelse(nrow(mtxdisdf_) >= 3, 3, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1456 c_ <- c_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1457 y <- length(d_) - (ifelse(nrow(mtxdisdf_) >= 4, 4, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1458 d_ <- d_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1459 y <- length(e_) - (ifelse(nrow(mtxdisdf_) >= 5, 5, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1460 e_ <- e_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1461 y <- length(f_) - (ifelse(nrow(mtxdisdf_) >= 6, 6, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1462 f_ <- f_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1463 y <- length(g_) - (ifelse(nrow(mtxdisdf_) >= 7, 7, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1464 g_ <- g_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1465 y <- length(h_) - (ifelse(nrow(mtxdisdf_) >= 8, 8, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1466 h_ <- h_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1467 y <- length(i_) - (ifelse(nrow(mtxdisdf_) >= 9, 9, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1468 i_ <- i_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1469 y <- length(j_) - (ifelse(nrow(mtxdisdf_) >= 10, 10, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1470 j_ <- j_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1471 y <- length(k_) - (ifelse(nrow(mtxdisdf_) >= 11, 11, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1472 k_ <- k_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1473 y <- length(l_) - (ifelse(nrow(mtxdisdf_) >= 12, 12, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1474 l_ <- l_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1475 y <- length(m_) - (ifelse(nrow(mtxdisdf_) >= 13, 13, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1476 m_ <- m_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1477 y <- length(n_) - (ifelse(nrow(mtxdisdf_) >= 14, 14, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1478 n_ <- n_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1479 y <- length(o_) - (ifelse(nrow(mtxdisdf_) >= 15, 15, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1480 o_ <- o_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1481 y <- length(p_) - (ifelse(nrow(mtxdisdf_) >= 16, 16, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1482 p_ <- p_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1483 y <- length(q_) - (ifelse(nrow(mtxdisdf_) >= 17, 17, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1484 q_ <- q_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1485 y <- length(r_) - (ifelse(nrow(mtxdisdf_) >= 18, 18, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1486 r_ <- r_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1487 y <- length(s_) - (ifelse(nrow(mtxdisdf_) >= 19, 19, nrow(mtxdisdf_)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1488 s_ <- s_[1:y]
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1489
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1490 rm(y)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1491
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1492 name_ <- c(a_, b_, c_, d_, e_, f_, g_, h_, i_, j_, k_, l_, m_, n_, o_, p_, q_, r_, s_)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1493 df_ <- data.frame(expand.grid(mtxdis), name_[1:seq_len(nrow(expand.grid(mtxdis)))])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1494 names(df_) <- c("dist.", "name_")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1495
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1496 rm(a_, b_, c_, d_, e_, f_, g_, h_, i_, j_, k_, l_, m_, n_, o_, p_, q_, r_, s_)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1497 rm(name_)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1498
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1499 q_ <- strsplit(df_$name_, " & ")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1500 mat_ <- matrix(unlist(q_), ncol = 2, byrow = TRUE)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1501 q_df_ <- as.data.frame(matrix(unlist(q_), ncol = 2, byrow = TRUE))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1502 df_ <- dplyr::bind_cols(df_, q_df_)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1503
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1504 rm(q_, mat_, q_df_)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1505
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1506 split_ <- strsplit(df_$V1, "_")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1507 v1_split_ <- as.data.frame(matrix(unlist(split_), ncol = 4, byrow = TRUE))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1508 split_ <- strsplit(df_$V2, "_")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1509 v2_split_ <- as.data.frame(matrix(unlist(split_), ncol = 4, byrow = TRUE))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1510
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1511 df_ <- dplyr::bind_cols(df_, v1_split_)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1512 df_ <- dplyr::bind_cols(df_, v2_split_)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1513 df_red_ <- subset(df_, V4...8 == V4...12 & V3...7 == V3...11)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1514 site_year_month_day <- rep(unique(qecbnato0_x$site_year_month_day), nrow(df_red_))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1515
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1516 df_red_ <- tibble::add_column(df_red_, site_year_month_day, .before = "dist.")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1517
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1518 rm(split_, v1_split_, v2_split_)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1519 rm(mtxdis, mtxdisdf_, df_, site_year_month_day)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1520
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1521 matri_list[[x]] <- df_red_
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1522 matri_list <<- matri_list
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1523
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1524 rm(df_red_, qecbnato0_x, x)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1525
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1526 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1527
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1528 matri_df <- do.call("rbind", matri_list)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1529
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1530 names(matri_df) <- c("site_year_month_day", "dist.", "name_", "name_left", "name_right", "Type.Bloc.left", "Face.left", "Numéro.Bloc.échantillon.left", "Quadrat.left", "Type.Bloc.right", "Face.right", "Numéro.Bloc.échantillon.right", "Quadrat.right")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1531
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1532 matri_df <<- matri_df
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1533
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1534 hist(matri_df$dist.)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1535
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1536 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1537
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1538 data_ <- dplyr::filter(qecbnato0, Type.Bloc == "Bloc mobile")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1539 matri_list <- vector("list", length(unique(data_$site_year_month_day)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1540
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1541 matri_fct_bmm(data = data_, conca = c(bret_egmp_basq_qecb, egmp_basq_qecb))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1542 hist(matri_df$dist., main = c(paste("Histo. of Bray (0-adjusted) dist. dissimilarity measures"), paste(" (sqrt transfo) - BMfs vs BMfi -")))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1543
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1544 matri_full_bm_bf_fi <- matri_df
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1545
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1546 rm(data_, matri_df, matri_list)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1547
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1548
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1549 #############################################################
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1550 # #
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1551 # Plot dissimilarity #
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1552 # #
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1553 #############################################################
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1554 ## plot
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1555
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1556 # activate line
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1557
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1558 matri_full_bm_bf_fs <- tidyr::separate(matri_full_bm_bf_fs, "site_year_month_day", into = c("departement", "Site", "Year", "Month", "Day"), remove = FALSE)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1559 matri_full_bm_bf_fs$Site <- paste0(matri_full_bm_bf_fs$departement, "_", matri_full_bm_bf_fs$Site)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1560 matri_full_bm_bf_fs <- subset(matri_full_bm_bf_fs, select = - c(departement))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1561
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1562 matri_full_bm_bf_fs <- tibble::add_column(matri_full_bm_bf_fs, Date = as.Date(paste0(matri_full_bm_bf_fs$Year, "-", matri_full_bm_bf_fs$Month, "-", matri_full_bm_bf_fs$Day), origin = "1970-01-01"), .after = "Site")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1563 matri_full_bm_bf_fs$Site <- as.factor(matri_full_bm_bf_fs$Site)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1564
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1565 matri_full_bm_bf_fi <- tidyr::separate(matri_full_bm_bf_fi, "site_year_month_day", into = c("departement", "Site", "Year", "Month", "Day"), remove = FALSE)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1566 matri_full_bm_bf_fi$Site <- paste0(matri_full_bm_bf_fi$departement, "_", matri_full_bm_bf_fi$Site)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1567 matri_full_bm_bf_fi <- subset(matri_full_bm_bf_fi, select = - c(departement))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1568 matri_full_bm_bf_fi <- tibble::add_column(matri_full_bm_bf_fi, Date = as.Date(paste0(matri_full_bm_bf_fi$Year, "-", matri_full_bm_bf_fi$Month, "-", matri_full_bm_bf_fi$Day), origin = "1970-01-01"), .after = "Site")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1569 matri_full_bm_bf_fi$Site <- as.factor(matri_full_bm_bf_fi$Site)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1570
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1571 # if error message "Error in .Call.graphics(C_palette2, .Call(C_palette2, NULL)) : invalid graphics state"
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1572
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1573
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1574 bf_fs_plot <- ggplot2::ggplot(matri_full_bm_bf_fs, ggplot2::aes(x = Site, y = dist.)) +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1575 ggplot2::geom_boxplot() +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1576 #geom_jitter(shape = 16, position=position_jitter(0.2)) +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1577 ggplot2::xlab("") +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1578 ggplot2::ylab("distance diss. BM.BF_FS") +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1579 ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, vjust = 0.5, hjust = 1))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1580
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1581 ggplot2::ggsave("distance_diss_BF_FS.png", bf_fs_plot, height = 4.5, width = 4)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1582
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1583 fs_fi_plot <- ggplot2::ggplot(matri_full_bm_bf_fi, ggplot2::aes(x = Site, y = dist.)) +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1584 ggplot2::geom_boxplot() +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1585 #geom_jitter(shape = 16, position=position_jitter(0.2)) +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1586 ggplot2::xlab("") +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1587 ggplot2::ylab("distance diss. BM_FS.FI") +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1588 ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, vjust = 0.5, hjust = 1))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1589
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1590 ggplot2::ggsave("distance_diss_FS_FI.png", fs_fi_plot, height = 4.5, width = 4)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1591
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1592 # issue with type de bloc, numéro de bloc and quadrat for df_ BM.BF_FS, cfr df_ left vs right variables doesn't give the right combination (variables with left vs right label in names come from the dissimilarity coefficient functions).
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1593 matri_full_bm_bf_fs$Quadrat <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1594 for (i in c(1:seq_len(nrow(matri_full_bm_bf_fs)))) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1595 ifelse(matri_full_bm_bf_fs$Type.Bloc.left[i] == "Bloc mobile", matri_full_bm_bf_fs$Quadrat[i] <- matri_full_bm_bf_fs$Quadrat.left[i], matri_full_bm_bf_fs$Quadrat[i] <- matri_full_bm_bf_fs$Quadrat.right[i])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1596 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1597 matri_full_bm_bf_fs$Numéro.Bloc <- NA
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1598 for (i in c(1:seq_len(nrow(matri_full_bm_bf_fs)))) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1599 ifelse(matri_full_bm_bf_fs$Type.Bloc.left[i] == "Bloc mobile", matri_full_bm_bf_fs$Numéro.Bloc[i] <- matri_full_bm_bf_fs$Numéro.Bloc.échantillon.left[i], matri_full_bm_bf_fs$Numéro.Bloc[i] <- matri_full_bm_bf_fs$Numéro.Bloc.échantillon.right[i])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1600 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1601
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1602 matri_full_bm_bf_fs <- tibble::add_column(matri_full_bm_bf_fs, site_year_month_day.q_BMnb = paste0(matri_full_bm_bf_fs$site_year_month_day, "_", matri_full_bm_bf_fs$Quadrat, "_", matri_full_bm_bf_fs$Numéro.Bloc), .after = "site_year_month_day")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1603 matri_full_bm_bf_fi <- tibble::add_column(matri_full_bm_bf_fi, site_year_month_day.q_BMnb = paste0(matri_full_bm_bf_fi$site_year_month_day, "_", matri_full_bm_bf_fi$Quadrat.left, "_", matri_full_bm_bf_fi$Numéro.Bloc.échantillon.left), .after = "site_year_month_day")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1604
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1605 colnames(matri_full_bm_bf_fs) <- paste("BM.BF_FS", colnames(matri_full_bm_bf_fs), sep = "_")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1606 matri_full_bm_bf_fs <- dplyr::rename(matri_full_bm_bf_fs, site_year_month_day.q_BMnb = BM.BF_FS_site_year_month_day.q_BMnb)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1607 colnames(matri_full_bm_bf_fi) <- paste("BM_FS.FI", colnames(matri_full_bm_bf_fi), sep = "_")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1608 matri_full_bm_bf_fi <- dplyr::rename(matri_full_bm_bf_fi, site_year_month_day.q_BMnb = BM_FS.FI_site_year_month_day.q_BMnb)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1609
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1610 matri_full <- dplyr::full_join(matri_full_bm_bf_fs[, c("site_year_month_day.q_BMnb", "BM.BF_FS_dist.")], matri_full_bm_bf_fi[, c("site_year_month_day.q_BMnb", "BM_FS.FI_dist.")])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1611
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1612 matri_full <- tidyr::separate(matri_full, "site_year_month_day.q_BMnb", into = c("departement", "Site", "Year", "Month", "Day", "Quadrat", "Bloc Mobile Number"), remove = FALSE)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1613 matri_full$Site <- paste0(matri_full$departement, "_", matri_full$Site)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1614 matri_full <- subset(matri_full, select = - c(departement))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1615 matri_full <- tibble::add_column(matri_full, Date = as.Date(paste0(matri_full$Year, "-", matri_full$Month, "-", matri_full$Day), origin = "1970-01-01"), .after = "Site")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1616
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1617 # Name for report/plot
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1618
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1619 matri_full <- tibble::add_column(matri_full, Site_bis = matri_full$Site, .after = "Site")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1620
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1621 matri_full$Site_bis <- ifelse(matri_full$Site == "GDMO_Locmariaquer", "Locmariaquer", matri_full$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1622 matri_full$Site_bis <- ifelse(matri_full$Site == "GDMO_BegLann", "Beg Lann", matri_full$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1623 matri_full$Site_bis <- ifelse(matri_full$Site == "FOUR_PlateauFour", "Plateau du Four", matri_full$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1624 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_GroinCou", "Groin du Cou", matri_full$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1625 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_PasEmsembert", "Le Pas d'Emsembert", matri_full$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1626 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_BreeBains", "La Brée-les-Bains", matri_full$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1627 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_PerreAntiochat", "Le Perré d'Antiochat", matri_full$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1628 matri_full$Site_bis <- ifelse(matri_full$Site == "EGMP_Chassiron", "Chassiron", matri_full$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1629 matri_full$Site_bis <- ifelse(matri_full$Site == "BASQ_FlotsBleusZP", "Les Flots Bleus / zone pêcheurs", matri_full$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1630 matri_full$Site_bis <- ifelse(matri_full$Site == "BASQ_FlotsBleusZF", "Les Flots Bleus / zone familles", matri_full$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1631 matri_full$Site_bis <- ifelse(matri_full$Site == "GONB_IlotStMichel", "Îlot Saint-Michel", matri_full$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1632 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_Quemenes", "Quéménès", matri_full$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1633 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_SeinGoulenez", "Île de Sein - Goulenez", matri_full$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1634 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_SeinKilaourou", "Île de Sein - Kilaourou", matri_full$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1635 matri_full$Site_bis <- ifelse(matri_full$Site == "ARMO_Verdelet", "Îlot du Verdelet", matri_full$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1636 matri_full$Site_bis <- ifelse(matri_full$Site == "ARMO_Piegu", "Piégu", matri_full$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1637 matri_full$Site_bis <- ifelse(matri_full$Site == "ARMO_Bilfot", "Pointe de Bilfot", matri_full$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1638 matri_full$Site_bis <- ifelse(matri_full$Site == "ARMO_IlePlate", "Île Plate", matri_full$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1639 matri_full$Site_bis <- ifelse(matri_full$Site == "PDMO_Perharidy", "Perharidy", matri_full$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1640 matri_full$Site_bis <- ifelse(matri_full$Site == "BRES_Keraliou", "Keraliou", matri_full$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1641 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_Mousterlin", "Pointe de Mousterlin", matri_full$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1642 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_StNicolasGlenan", "Saint-Nicolas des Glénan", matri_full$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1643 matri_full$Site_bis <- ifelse(matri_full$Site == "FINS_AnseRoz", "Pointe de l'Anse du Roz", matri_full$Site_bis)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1644
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1645 saveRDS(matri_full, "matri_full.RDS")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1646
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1647 #############################################################
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1648 # #
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1649 # Plot the dissimilarity per site #
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1650 # #
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1651 #############################################################
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1652 ## plot dissimilarity coefficient
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1653
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1654 matri_full$Year <- as.integer(matri_full$Year)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1655 matri_full$Month <- as.integer(matri_full$Month)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1656 matri_full$Day <- as.integer(matri_full$Day)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1657
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1658
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1659 ## BM_FS.FI_dist => mobile boulder upper vs lower faces
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1660
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1661 # Stats
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1662
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1663 bm_fs_fi_dist_stat <- matri_full %>% dplyr::group_by(Site, Site_bis, Date, Year, Month, Day) %>% dplyr::summarize(BM_FS.FI_dist.moy = mean(BM_FS.FI_dist., na.rm = TRUE), BM_FS.FI_dist.et = sd(BM_FS.FI_dist., na.rm = TRUE), BM_FS.FI_dist.med = median(BM_FS.FI_dist., na.rm = TRUE), BM_FS.FI_dist.min = min(BM_FS.FI_dist., na.rm = TRUE), BM_FS.FI_dist.max = max(BM_FS.FI_dist., na.rm = TRUE), nb. = dplyr::n(), nb.notNa = sum(!is.na(BM_FS.FI_dist.)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1664
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1665 bm_fs_fi_dist_stat <- dplyr::ungroup(bm_fs_fi_dist_stat)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1666
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1667 # Quality scale based on quartiles
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1668
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1669 if (choice == "N") {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1670 one <- round(mean(unlist(dplyr::filter(matri_full, BM_FS.FI_dist. <= quantile(matri_full$BM_FS.FI_dist., 0.25, na.rm = TRUE))["BM_FS.FI_dist."])), digits = 3)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1671 two <- round(mean(unlist(dplyr::filter(matri_full, BM_FS.FI_dist. > quantile(matri_full$BM_FS.FI_dist., 0.25, na.rm = TRUE) & BM_FS.FI_dist. <= quantile(matri_full$BM_FS.FI_dist., 0.5, na.rm = TRUE))["BM_FS.FI_dist."])), digits = 3)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1672 three <- round(mean(unlist(dplyr::filter(matri_full, BM_FS.FI_dist. > quantile(matri_full$BM_FS.FI_dist., 0.5, na.rm = TRUE) & BM_FS.FI_dist. <= quantile(matri_full$BM_FS.FI_dist., 0.75, na.rm = TRUE))["BM_FS.FI_dist."])), digits = 3)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1673 four <- round(mean(unlist(dplyr::filter(matri_full, BM_FS.FI_dist. > quantile(matri_full$BM_FS.FI_dist., 0.75, na.rm = TRUE))["BM_FS.FI_dist."])), digits = 3)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1674 }else {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1675 one <- 0.47
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1676 two <- 0.7
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1677 three <- 0.83
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1678 four <- 0.98
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1679 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1680
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1681 val_xmax <- as.Date(paste0(as.character(choice_date + 1), "-01-01"), origin = "1970-01-01")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1682
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1683 for (i in c(1:length(unique(bm_fs_fi_dist_stat$Site)))) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1684
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1685 df1 <- dplyr::filter(bm_fs_fi_dist_stat, bm_fs_fi_dist_stat$Site == unique(bm_fs_fi_dist_stat$Site)[i])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1686
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1687 bm_fs_fi_plot <- ggplot2::ggplot() +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1688 ggplot2::geom_point(ggplot2::aes(x = bm_fs_fi_dist_stat$Date, y = bm_fs_fi_dist_stat$BM_FS.FI_dist.med), col = "grey") +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1689 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = - 0.1, ymax = one, fill = "blue"), alpha = 0.3) +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1690 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = one, ymax = two, fill = "green"), alpha = 0.3) +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1691 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = two, ymax = three, fill = "yellow"), alpha = 0.3) +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1692 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = three, ymax = four, fill = "orange"), alpha = 0.3) +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1693 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = four, ymax = 1.1, fill = "red"), alpha = 0.3) +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1694 ggplot2::scale_fill_manual(values = c("#FF0000", "#F59404", "#18E125", "#1A1AE8", "#FAFA15")) +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1695 ggplot2::geom_pointrange(ggplot2::aes(x = df1$Date, y = df1$BM_FS.FI_dist.med, ymin = df1$BM_FS.FI_dist.min, ymax = df1$BM_FS.FI_dist.max), col = "black") +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1696 ggplot2::xlab("Date") +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1697 ggplot2::ylab("Coef dissim BM FS-FI") +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1698 ggplot2::ggtitle(unique(df1$Site_bis)) +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1699 ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, vjust = 0.5, hjust = 1), legend.position = "none")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1700
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1701 ggplot2::ggsave(paste0("fs_fi_", df1$Site, ".png"), device = "png", bm_fs_fi_plot, height = 3, width = 3.5)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1702
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1703 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1704
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1705 rm(df1, four, i, one, three, two, xmax_, xmin_, ymax_, ymin_)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1706
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1707
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1708 ## BM.BF_FS_dist => mobile boulder vs fixed boulder upper faces
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1709
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1710 # Stats
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1711
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1712 bm_bf_fs_dist_stat <- matri_full %>% dplyr::group_by(Site, Site_bis, Date, Year, Month, Day) %>% dplyr::summarize(BM.BF_FS_dist.moy = mean(BM.BF_FS_dist., na.rm = TRUE), BM.BF_FS_dist.et = sd(BM.BF_FS_dist., na.rm = TRUE), BM.BF_FS_dist.med = median(BM.BF_FS_dist., na.rm = TRUE), BM.BF_FS_dist.min = min(BM.BF_FS_dist., na.rm = TRUE), BM.BF_FS_dist.max = max(BM.BF_FS_dist., na.rm = TRUE), nb. = dplyr::n(), nb.notNa = sum(!is.na(BM.BF_FS_dist.)))
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1713
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1714 bm_bf_fs_dist_stat <- dplyr::ungroup(bm_bf_fs_dist_stat)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1715
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1716 # Quality scale based on quartiles
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1717
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1718 if (choice == "N") {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1719 one <- round(mean(unlist(dplyr::filter(matri_full, BM.BF_FS_dist. <= quantile(matri_full$BM.BF_FS_dist., 0.25, na.rm = TRUE))["BM.BF_FS_dist."])), digits = 3)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1720 two <- round(mean(unlist(dplyr::filter(matri_full, BM.BF_FS_dist. > quantile(matri_full$BM.BF_FS_dist., 0.25, na.rm = TRUE) & BM.BF_FS_dist. <= quantile(matri_full$BM.BF_FS_dist., 0.5, na.rm = TRUE))["BM.BF_FS_dist."])), digits = 3)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1721 three <- round(mean(unlist(dplyr::filter(matri_full, BM.BF_FS_dist. > quantile(matri_full$BM.BF_FS_dist., 0.5, na.rm = TRUE) & BM.BF_FS_dist. <= quantile(matri_full$BM.BF_FS_dist., 0.75, na.rm = TRUE))["BM.BF_FS_dist."])), digits = 3)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1722 four <- round(mean(unlist(dplyr::filter(matri_full, BM.BF_FS_dist. > quantile(matri_full$BM.BF_FS_dist., 0.75, na.rm = TRUE))["BM.BF_FS_dist."])), digits = 3)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1723
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1724 }else {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1725 one <- 0.19
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1726 two <- 0.32
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1727 three <- 0.455
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1728 four <- 0.735
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1729 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1730 # Plot
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1731
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1732 for (i in c(1:length(unique(bm_bf_fs_dist_stat$Site)))) {
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1733
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1734 df1 <- dplyr::filter(bm_bf_fs_dist_stat, bm_bf_fs_dist_stat$Site == unique(bm_bf_fs_dist_stat$Site)[i])
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1735
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1736 bm_bf_fs_plot <- ggplot2::ggplot() +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1737 ggplot2::geom_point(ggplot2::aes(x = bm_bf_fs_dist_stat$Date, y = bm_bf_fs_dist_stat$BM.BF_FS_dist.med), col = "grey") +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1738 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = - 0.1, ymax = one, fill = "red"), alpha = 0.3) +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1739 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = one, ymax = two, fill = "orange"), alpha = 0.3) +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1740 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = two, ymax = three, fill = "yellow"), alpha = 0.3) +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1741 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = three, ymax = four, fill = "green"), alpha = 0.3) +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1742 ggplot2::geom_rect(ggplot2::aes(xmin = as.Date("2013-01-01", origin = "1970-01-01"), xmax = val_xmax, ymin = four, ymax = 1.1, fill = "blue"), alpha = 0.3) +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1743 ggplot2::scale_fill_manual(values = c("#FF0000", "#F59404", "#18E125", "#1A1AE8", "#FAFA15")) +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1744 ggplot2::geom_pointrange(ggplot2::aes(x = df1$Date, y = df1$BM.BF_FS_dist.med, ymin = df1$BM.BF_FS_dist.min, ymax = df1$BM.BF_FS_dist.max), col = "black") +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1745 ggplot2::xlab("Date") +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1746 ggplot2::ylab("Coef dissim BM-BF FS") +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1747 ggplot2::ggtitle(unique(df1$Site_bis)) +
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1748 ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, vjust = 0.5, hjust = 1), legend.position = "none")
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1749
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1750 ggplot2::ggsave(paste0("bm_bf_", df1$Site, ".png"), device = "png", bm_bf_fs_plot, height = 3, width = 3.5)
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1751
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1752 }
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1753
a8924f69348d planemo upload for repository https://github.com/Marie59/champ_blocs commit 0d86db7d42b608c386a54500064f5f9c9d7019a4
ecology
parents:
diff changeset
1754 rm(df1, four, i, one, three, two, xmax_, xmin_, ymax_, ymin_)