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annotate div_index.r @ 1:83a4d3b47184 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 16:48:40 +0000
parents 89f977a3a256
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89f977a3a256 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 #####Load arguments
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15 args <- commandArgs(trailingOnly = TRUE)
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17 #####Import data
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19 if (length(args) < 1) {
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20 stop("This tool needs at least 1 argument")
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21 }else {
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22 qecnato0 <- args[1]
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24 }
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26 qecnato0 <- readRDS(qecnato0)
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29 # first, create vector (4) for qecb and fishing by region (same as above)
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31 bret_egmp_basq_qecb <- c(
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32 "X..algues.brunes",
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33 "X..algues.rouges",
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34 "X..algues.vertes",
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35 "X..Cladophora",
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36 "X..Lithophyllum",
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37 "Nb.Littorina.obtusata",
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38 "Nb.Gibbula.cineraria",
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39 "Nb.Gibbula.pennanti",
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40 "Nb.Gibbula.umbilicalis",
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41 "Nb.Phallusia.mamillata",
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42 "Nb.Tethya.aurantium",
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43 "Nb.Spirobranchus.lamarckii.total",
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44 "Nb.spirorbis.total",
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45 "X..Eponges",
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46 "X..Ascidies.Coloniales",
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47 "X..Ascidies.Solitaires",
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48 "X..Bryozoaires.Dresses",
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49 "X..Balanes.Vivantes"
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50 #, "X..Recouvrement.Sediment"
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51 #, "X..Roche.Nue"
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52 #, "X..Surface.Accolement"
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53 )
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54
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55 egmp_basq_qecb <- c("Nb.Crassostrea.gigas", "Nb.Ostrea.edulis", "X..Mytilus.sp.", "X..Hermelles", "X..Hydraires")
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56
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57 bret_egmp_basq_fishing <- c("Nb.Cancer.pagurus..Tourteau.",
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58 "Nb.Necora.puber..Etrille.",
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59 "Nb.Carcinus.maenas..Crabe.vert.",
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60 "Nb.Nucella.lapilus..Pourpre.",
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61 "Nb.Galathea..Galathées.",
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62 "Nb.Lophozozymus.incisus..ancien.Xantho.incisus.",
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63 "Nb.Palaemon.sp..Crevette.bouquet.ou.crevette.rose.",
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64 "Nb.Haliotis.tuberculata..Ormeau.",
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65 "Nb.Littorina.littorea..Bigorneau.",
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66 "Nb.Xantho.pilipes..Xanthe.poilu.",
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67 "Nb.Mimachlamys.varia..Pétoncle.noir.")
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68
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69 egmp_basq_fishing <- c("Nb.Eriphia.verrucosa..Crabe.verruqueux.", "Nb.Octopus.vulgaris..Poulpe.", "Nb.Paracentrotus.lividus..Oursin.", "Nb.Stramonita.haemastoma..Pourpre.bouche.de.sang.")
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71 # here I can choose to either replace spirorbis and/or spirobranchus by their log10 transformation in bret_egmp_basq_qecb vector
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72 bret_egmp_basq_qecb <- replace(bret_egmp_basq_qecb, bret_egmp_basq_qecb == "Nb.spirorbis.total", "log10.Nb.spirorbis.total")
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74 ## Diversity index
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77 # adiv contains two main functions for species diversity indices: speciesdiv, which includes widely used indices such as species richness and the Shannon index, and divparam, which includes indices that have a parameter to control the importance given to rare versus abundant species in diversity measurements (Pavoine (2020) - adiv: An r package to analyse biodiversity in ecology).
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79 # NB: just like for dissimilarity distance matrices, no sense to use the "fishing" variable lists, because either they are present for the bloc mobile and not for the bloc fixe (therefore false higher diversity for bloc mobile), either they are repeated between face supérieure and face inférieure of bloc mobile.
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81 # function in a loop
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83 row.names(qecnato0) <- c(paste0(qecnato0$region.site_year_month_day, "_", qecnato0$Quadrat.bis, "_", qecnato0$Type.Bloc, "_", qecnato0$Numéro.Bloc.échantillon, "_", qecnato0$Face))
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84
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85 # later on I can copy-paste above code to recreate variable names vector
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86 #bret_egmp_basq_qecb
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87 #egmp_basq_qecb
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88 #Bret_EGMP.BASQ_fishing
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89 #EGMP.BASQ_fishing
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90
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91 # remove boulder variables
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92 bret_egmp_basq_qecb <- bret_egmp_basq_qecb[! bret_egmp_basq_qecb %in% c("X..Recouvrement.Sediment", "X..Roche.Nue", "X..Surface.Accolement")]
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93
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94 qecnato0$period <- as.character(qecnato0$period)
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95 qecnato0$Face <- as.character(qecnato0$Face)
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96
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97 div_list <- vector("list", length(unique(qecnato0$site_year_month_day)))
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98 library(dplyr)
0
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99 for (i in c(1:nrow(qecnato0))) {
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100 div_i <- dplyr::filter(qecnato0, site_year_month_day == qecnato0$site_year_month_day[i])
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101
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102 ifelse(unique(div_i$region) == "Bretagne", var. <- c(bret_egmp_basq_qecb), var. <- c(bret_egmp_basq_qecb, egmp_basq_qecb)) # Qu. : Why can't R's ifelse statements return vectors? => you can circumvent the problem if you assign the result inside the ifelse.
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103
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104 #8 remove empty row cfr: In speciesdiv(div_i[, var.]) & divparam(div_i[, var.]) : empty communities should be discarded
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105 div_i <- dplyr::filter(div_i, rowSums(div_i[, var.]) > 0)
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106
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107 div_i_speciesdiv <- adiv::speciesdiv(div_i[, var.])
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108 adiv_i_df <- data.frame(div_i_speciesdiv)
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109
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110 div_i_divparam <- adiv::divparam(div_i[, var.], q = c(0, 0.25, 0.5, 1, 2, 4, 8)) # When q increases, abundant species are overweighted compared to rare species, we thus expect that the evenness in species weights decreases.
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111
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112
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113 par(mfrow = c (1, 1))
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114 plot(adiv::divparam(div_i[, var.], q = 0), main = unique(div_i$site_year_month_day))
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115 plot(adiv::divparam(div_i[, var.], q = 0:10), legend = FALSE, main = unique(div_i$site_year_month_day))
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116
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117 adiv_i_df$x <- div_i_divparam$div$`1`
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118 colnames(adiv_i_df)[which(colnames(adiv_i_df) == "x")] <- paste0("Para. ISD, q = ", div_i_divparam$q[1], " (equi. richness)")
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119 adiv_i_df$x <- div_i_divparam$div$`2`
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120 colnames(adiv_i_df)[which(colnames(adiv_i_df) == "x")] <- paste0("Para. ISD, q = ", div_i_divparam$q[2])
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121 adiv_i_df$x <- div_i_divparam$div$`3`
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122 colnames(adiv_i_df)[which(colnames(adiv_i_df) == "x")] <- paste0("Para. ISD, q = ", div_i_divparam$q[3])
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123 adiv_i_df$x <- div_i_divparam$div$`4`
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124 colnames(adiv_i_df)[which(colnames(adiv_i_df) == "x")] <- paste0("Para. ISD, q = ", div_i_divparam$q[4])
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125 adiv_i_df$x <- div_i_divparam$div$`5`
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126 colnames(adiv_i_df)[which(colnames(adiv_i_df) == "x")] <- paste0("Para. ISD, q = ", div_i_divparam$q[5], " (equi. Simpson)")
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127 adiv_i_df$x <- div_i_divparam$div$`6`
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128 colnames(adiv_i_df)[which(colnames(adiv_i_df) == "x")] <- paste0("Para. ISD, q = ", div_i_divparam$q[6])
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129 adiv_i_df$x <- div_i_divparam$div$`7`
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130 colnames(adiv_i_df)[which(colnames(adiv_i_df) == "x")] <- paste0("Para. ISD, q = ", div_i_divparam$q[7])
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131
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132 # plot
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133 par(mfrow = c(3, 2))
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134 sapply(names(adiv_i_df[, c(1, 8, 2, 3, 12, 4:7, 9:11, 13:ncol(adiv_i_df))]),
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135 function(cname) {
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136 png(paste0(cname, "_histo.png"))
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137 hist(adiv_i_df[, c(1, 8, 2, 3, 12, 4:7, 9:11, 13:ncol(adiv_i_df))][[cname]], main = "", xlab = cname, breaks = length(unique(adiv_i_df[, c(1, 8, 2, 3, 12, 4:7, 9:11, 13:ncol(adiv_i_df))][[cname]])))
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138 dev.off()
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139 }
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140
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141 )
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142 par(mfrow = c(1,1))
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143
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144 div_list[[i]] <- adiv_i_df
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145
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146 rm(div_i, adiv_i_df, div_i_speciesdiv, div_i_divparam)
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147
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148 }
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149
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150 # for the error message due to richness NA data => 35 observations in 21 surveys; no reason to remove these data "...remo", was checked in the complete script.
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151
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152
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153 div_df <- do.call("rbind", div_list)
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154
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155
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156 # There is an issue with region.terri that are merged with no "_" ...
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157
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158 div_df <- tibble::add_column(div_df, rownames. = rownames(div_df), .before = "richness")
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159 div_df <- tidyr::separate(div_df, rownames., into = c("region.terri.", "site_year_month_day", "Quadrat.bis", "Type.Bloc", "Numéro.Bloc.échantillon", "Face"), sep = "_")
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160
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161 # I therefore add these lines to solve that issue
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162
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163 div_df <- tibble::add_column(div_df, terri. = substring(div_df$region.terri., nchar(div_df$region.terri.)-3), .after = "region.terri.")
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164
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165 div_df$region.terri. <- substring(div_df$region.terri., 1, nchar(div_df$region.terri)-4)
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166 div_df <- dplyr::rename(div_df, region = region.terri.)
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167
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168 div_df$site_year_month_day <- paste0(div_df$terri., "_", div_df$site_year_month_day)
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169 div_df <- subset(div_df, select = -c(terri.))
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170
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171 div_df$Type.Bloc <- as.factor(div_df$Type.Bloc)
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172 div_df$Face <- as.factor(div_df$Face)
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173 div_df$Numéro.Bloc.échantillon <- as.integer(div_df$Numéro.Bloc.échantillon)
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174
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175 saveRDS(div_df, "div_df.RDS")
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176 write.table(div_df, "Valeurs_stat.tabular", row.names = FALSE, quote = FALSE, sep = "\t", dec = ".", fileEncoding = "UTF-8")