Mercurial > repos > ecology > ecology_homogeneity_normality

annotate graph_link_var.r @ 0:9f679060051a draft

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"planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
author ecology
date Tue, 27 Jul 2021 16:56:15 +0000
parents
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0
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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1 #Rscript
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2
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3 ################################################
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4 ## Link between variables and themselves ##
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5 ################################################
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6
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7 #####Packages : ggplot2
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8 # Cowplot
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9 # Car
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10 # faraway
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11 # dplyr
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12 # GGally
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13 # FactoMiner
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14 # factoextra
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15 # ggcorrplot
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17 #####Load arguments
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19 args <- commandArgs(trailingOnly = TRUE)
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21 if (length(args) == 0) {
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22 stop("This tool needs at least one argument")
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23 }else{
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24 table <- args[1]
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25 hr <- args[2]
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26 colli <- as.logical(args[3])
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27 vif <- as.logical(args[4])
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28 pca <- as.logical(args[5])
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29 interr <- as.logical(args[6])
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30 auto <- as.logical(args[7])
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31 spe <- as.numeric(args[8])
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32 col <- as.numeric(strsplit(args[9], ",")[[1]])
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33 var <- as.numeric(args[10])
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34 var2 <- as.numeric(args[11])
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35 var4 <- as.numeric(args[12])
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36 }
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38 if (hr == "false") {
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39 hr <- FALSE
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40 }else{
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41 hr <- TRUE
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42 }
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44 if (length(col) == 1) {
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45 stop("Please select two or more numerical columns")
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46 }
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48 #####Import data
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49 data <- read.table(table, sep = "\t", dec = ".", header = hr, fill = TRUE, encoding = "UTF-8")
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50 if (vif | pca) {
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51 data_active <- data[col]
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52 #Define the active individuals and the active variables for the PCA
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53 }
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55 if (colli | interr) {
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56 colspe <- colnames(data)[spe]
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57 }
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59 if (colli) {
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60 data_num <- data[col]
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61 data_num$species <- data[, spe]
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62 data_num <- data_num[grep("^$", data_num$spe, invert = TRUE), ]
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63 }
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64
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65 if (interr | auto) {
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66 colvar <- colnames(data)[var]
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67 }
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69 if (interr) {
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70 colvar2 <- colnames(data)[var2]
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71 colvar4 <- colnames(data)[var4]
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72 }
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74 #####Your analysis
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76 ####Independence of the observations####
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78 acf_tb <- function(data, var) {
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79 obj <- acf(data[, var], na.action = na.pass)
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80 return(obj)
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81 }
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83 acf_df <- function(data, var) {
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85 tb <- data.frame(acf = acf_tb(data, var)$acf, lag = acf_tb(data, var)$lag)
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87 return(tb) # Lag: intervalle temporel entre mesures, fréquence à laquelle on mesure l'auto corrélation.
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88 # ACF: indépendance temporelle
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89 }
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91 autocorr <- function(var1, var2) {
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92 cat("\nACF\n", var2$acf, file = "acf.txt", fill = 1, append = TRUE)
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93 graph <- ggplot2::ggplot() +
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94 ggplot2::geom_bar(ggplot2::aes(x = var2$lag, y = var2$acf), stat = "identity", position = "identity", fill = "midnightblue") +
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95 ggplot2::geom_hline(mapping = ggplot2::aes(yintercept = qnorm((1 + 0.95) / 2) / sqrt(var1$n.used)),
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96 linetype = "dashed") + # calcul interval de confiance à 95% sans correction du bruit blanc.
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97 ggplot2::geom_hline(mapping = ggplot2::aes(yintercept = -qnorm((1 + 0.95) / 2) / sqrt(var1$n.used)), linetype = "dashed") + ggplot2::labs(title = "Autocorrelation") + ggplot2::xlab("lag") + ggplot2::ylab("acf")
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98 ggplot2::theme(plot.title = ggplot2::element_text(hjust = 0.5))
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100 ggplot2::ggsave("autocorrelation.png", graph)
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101 }
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
102
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
103 ####Interractions####
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
104
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
105 graph <- function(data, var1, var2, var3) {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
106 graph <- ggplot2::ggplot(data, ggplot2::aes_string(x = var1, y = var2, group = var3, color = var3)) +
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
107 ggplot2::geom_point() +
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
108 ggplot2::geom_smooth(method = lm, se = FALSE) +
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
109 ggplot2::theme(plot.title = ggplot2::element_text(color = "black", size = 12, face = "bold"))
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
110
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
111 return(graph)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
112 }
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
113
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
114 # Put multiple panels
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
115 interraction <- function(data, var1, var2, var3, var4) {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
116 cat("\nSpecies\n", spe, file = "Species.txt", fill = 1, append = TRUE)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
117 if (mult1) {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
118 for (spe in unique(data[, var3])) {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
119 data_cut <- data[data[, var3] == spe, ]
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
120 mult_graph <- graph(data_cut, var1, var2, var3) + ggplot2::facet_grid(cols = ggplot2::vars(data_cut[, var4]), scales = "free") +
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
121 cowplot::background_grid(major = "xy", minor = "none") +
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
122 cowplot::panel_border() + ggplot2::ggtitle("Interactions")
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
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123
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
124 ggplot2::ggsave(paste("interaction_of_", spe, ".png"), mult_graph, width = 10, height = 7)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
125 }
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
126 }else{
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
127 mult_graph <- graph(data, var1, var2, var3) + ggplot2::facet_grid(rows = ggplot2::vars(data[, var3]), cols = ggplot2::vars(data[, var4]), scales = "free") +
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
128 cowplot::background_grid(major = "xy", minor = "none") +
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
129 cowplot::panel_border() + ggplot2::ggtitle("Interactions")
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
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130
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
131 ggplot2::ggsave("interraction.png", mult_graph)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
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132 }
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
133 }
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
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134
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
135 ####Collinearity among covariates####
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
136 # Create the plots
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
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137
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
138 coli <- function(data, var) {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
139 if (mult2) {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
140 cat("\nThere is not enough data on these species they appear too few times in the tabular-file\n", file = "Data.txt", fill = 1, append = TRUE)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
141 for (spe in unique(data$species)) {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
142 nb_spe <- sum(data$species == spe)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
143 if (nb_spe <= 2) {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
144 cat(spe, file = "Data.txt", fill = 1, append = TRUE)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
145 }else{
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
146 data_cut <- data[data$species == spe, ]
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
147 nb <- ncol(data_cut)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
148 data_num <- data_cut[, -nb]
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
149 graph <- GGally::ggpairs(data_num, ggplot2::aes(color = data_cut$species),
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
150 lower = list(continuous = "points"), axisLabels = "internal")
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
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151
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
152 ggplot2::ggsave(paste0("collinarity_of_", spe, ".png"), graph, width = 20, height = 15)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
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153 }
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
154 }
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
155
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
156 }else{
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
157 nb <- ncol(data)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
158 data_cut <- data[, -nb]
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
159 graph <- GGally::ggpairs(data_cut, ggplot2::aes(color = data[, var]),
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
160 lower = list(continuous = "points"), axisLabels = "internal") +
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
161 ggplot2::scale_colour_manual(values = c("#00AFBB", "#E7B800", "#FC4E07")) +
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
162 ggplot2::scale_fill_manual(values = c("#00AFBB", "#E7B800", "#FC4E07"))
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
163
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
164 ggplot2::ggsave("collinarity.png", graph)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
165 }
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
166 }
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
167
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
168 ####PCA method####
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
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169
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
170 plot_pca <- function(data) {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
171 #Correlation circle
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
172 graph_corr <- factoextra::fviz_pca_var(active_data(data), col.var = "cos2",
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
173 gradient.cols = c("#00AFBB", "#E7B800", "#FC4E07"),
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
174 repel = TRUE #Avoid text overlap
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
175 )
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
176 ggplot2::ggsave("Pca_circle.png", graph_corr)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
177 }
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
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178
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
179 plot_qual <- function(data) {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
180 #PCA results for variables
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
181 var <- factoextra::get_pca_var(active_data(data))
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
182
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
183 #representation quality
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
184 graph_quality <- ggcorrplot::ggcorrplot(var$cos2[!apply(var$cos2, 1, anyNA), ], method = "circle",
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
185 ggtheme = ggplot2::theme_gray,
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
186 colors = c("#00AFBB", "#E7B800", "#FC4E07"))
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
187
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
188 ggplot2::ggsave("Pca_quality.png", graph_quality)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
189 }
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
190
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
191 #### Variance inflation factor ####
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
192
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ecology
parents:
diff changeset
193 myvif <- function(mod) {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
194 v <- vcov(mod)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
195 assign <- attributes(model.matrix(mod))$assign
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
196 if (names(coefficients(mod)[1]) == "(Intercept)") {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
197 v <- v[-1, -1]
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
198 assign <- assign[-1]
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
199 } else warning("No intercept: vifs may not be sensible.")
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
200 terms <- labels(terms(mod))
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
201 n_terms <- length(terms)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
202 if (n_terms < 2) stop("The model contains fewer than 2 terms")
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
203 if (length(assign) > dim(v)[1]) {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
204 diag(tmp_cor) <- 0
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
205 if (any(tmp_cor == 1.0)) {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
206 return("Sample size is too small, 100% collinearity is present")
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
207 } else {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
208 return("Sample size is too small")
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
209 }
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
210 }
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
211 r <- cov2cor(v)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
212 detr <- det(r)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
213 result <- matrix(0, n_terms, 3)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
214 rownames(result) <- terms
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
215 colnames(result) <- c("GVIF", "Df", "GVIF^(1/2Df)")
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
216 for (term in 1:n_terms) {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
217 subs <- which(assign == term)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
218 result[term, 1] <- det(as.matrix(r[subs, subs])) * det(as.matrix(r[-subs, -subs])) / detr
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
219 result[term, 2] <- length(subs)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
220 }
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
221 if (all(result[, 2] == 1)) {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
222 result <- data.frame(GVIF = result[, 1])
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
223 } else {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
224 result[, 3] <- result[, 1] ^ (1 / (2 * result[, 2]))
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
225 }
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
226 invisible(result)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
227 }
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
228 corvif1 <- function(dataz) {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
229 dataz <- as.data.frame(dataz)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
230 #correlation part
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
231 tmp_cor <- cor(dataz, use = "complete.obs")
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
232 return(tmp_cor)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
233 }
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
234 corvif2 <- function(dataz) {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
235 dataz <- as.data.frame(dataz)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
236 #vif part
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
237 form <- formula(paste("fooy ~ ", paste(strsplit(names(dataz), " "), collapse = " + ")))
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
238 dataz <- data.frame(fooy = 1, dataz)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
239 lm_mod <- lm(form, dataz)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
240
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
241 return(myvif(lm_mod))
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
242 }
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
243
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
244 #Autocorrelation
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
245 if (auto) {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
246 obj1 <- acf_tb(data, var = colvar)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
247 obj2 <- acf_df(data, var = colvar)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
248 autocorr(var1 = obj1, var2 = obj2)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
249 }
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
250
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
251 if (interr) {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
252 #Interractions
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
253 mult1 <- ifelse(length(unique(data[, colspe])) <= 6, FALSE, TRUE)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
254 interraction(data, var1 = colvar, var2 = colvar2, var3 = colspe, var4 = colvar4)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
255 }
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
256
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
257 #Collinearity
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
258 if (colli) {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
259 mult2 <- ifelse(length(unique(data[, spe])) < 3, FALSE, TRUE)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
260 coli(data = data_num, var = spe)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
261 }
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
262
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
263 #PCA
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
264 if (pca) {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
265 active_data <- function(data) {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
266 #Calcul of PCA for the active data
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
267 res_pca <- FactoMineR::PCA(data, graph = FALSE)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
268
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
269 return(res_pca)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
270 }
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
271
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
272 #eigenvalue
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
273 eig_val <- capture.output(factoextra::get_eigenvalue(active_data(data_active)))
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
274
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
275 cat("\nwrite table with eigenvalue. \n--> \"", paste(eig_val, "\"\n", sep = ""), file = "valeurs.txt", sep = "", append = TRUE)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
276
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
277 plot_pca(data_active)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
278 plot_qual(data_active)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
279 }
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
280
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
281 #VIF
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
282 if (vif) {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
283 #Compute 2 tables#
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
284 tb_corr <- as.data.frame(corvif1(dataz = data_active))
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
285 tb_corr <- cbind(x = rownames(tb_corr), tb_corr)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
286 tb_vif <- corvif2(dataz = data_active)
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
287
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
288 write.table(tb_corr, "corr.tabular", row.names = FALSE, quote = FALSE, sep = "\t", dec = ".", fileEncoding = "UTF-8")
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
289
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
290 if (all(is.na(tb_vif))) {
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
291 tb_vif <- NULL
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
292 cat("Vif couldn't be calculated, selected data isn't correlated")
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
293 }else{
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
294 write.table(tb_vif, "vif.tabular", row.names = FALSE, quote = FALSE, sep = "\t", dec = ".", fileEncoding = "UTF-8")
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
295 }
9f679060051a "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
296 }