Mercurial > repos > ecology > ecology_stat_presence_abs

annotate graph_pres_abs_abund.r @ 1:9a2e0195bb43 draft default tip

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"planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
author ecology
date Fri, 13 Aug 2021 18:18:21 +0000
parents e5552099d0e3
children
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e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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1 #Rscript
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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3 #########################################################
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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4 ## Presence abscence and abundance in environment ##
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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5 #########################################################
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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6
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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7 #####Packages : ggplot2
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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8 # vegan
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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9
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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10 #####Load arguments
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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12 args <- commandArgs(trailingOnly = TRUE)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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14 if (length(args) < 5) {
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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15 stop("This tool needs at least 5 arguments")
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
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16 }else{
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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17 table <- args[1]
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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18 hr <- args[2]
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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19 abundance <- as.logical(args[3])
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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20 presabs <- as.logical(args[4])
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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21 rarefaction <- as.logical(args[5])
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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22 lat <- as.numeric(args[6])
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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23 long <- as.numeric(args[7])
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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24 ind <- as.character(args[8])
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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25 loc <- as.numeric(args[9])
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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26 num <- as.character(args[10])
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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27 spe <- as.numeric(args[11])
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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28 abond <- as.numeric(args[12])
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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29 }
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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31 if (hr == "false") {
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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32 hr <- FALSE
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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33 }else{
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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34 hr <- TRUE
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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35 }
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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37 #####Import data
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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38 data <- read.table(table, sep = "\t", dec = ".", header = hr, fill = TRUE, encoding = "UTF-8")
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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40 if (abundance) {
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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41 collat <- colnames(data)[lat]
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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42 collong <- colnames(data)[long]
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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43 }
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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44
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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45 if (presabs) {
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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46 colloc <- colnames(data)[loc]
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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47 }
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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49 if (presabs | rarefaction | abundance) {
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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50 colabond <- colnames(data)[abond]
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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51 colspe <- colnames(data)[spe]
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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52 data <- data[grep("^$", data[, colspe], invert = TRUE), ]
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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53 }
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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54
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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55 #####Your analysis
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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57 ####The abundance in the environment####
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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58
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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59 ##Representation of the environment##
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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60
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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61 ## Mapping
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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62 graph_map <- function(data, collong, collat, colabond, ind, colspe) {
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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63 cat("\nCoordinates range\n\nLatitude from ", min(data[, collat], na.rm = TRUE), " to ", max(data[, collat], na.rm = TRUE), "\nLongitude from ", min(data[, collong], na.rm = TRUE), " to ", max(data[, collong], na.rm = TRUE), file = "Data_abund.txt", fill = 1, append = TRUE)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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64 if (mult0) {
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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65 mappy <- ggplot2::ggplot(data, ggplot2::aes_string(x = collong, y = collat, cex = colabond, color = colspe)) +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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66 ggplot2::geom_point() + ggplot2::ggtitle(paste("Abundance of", ind, "in the environment")) + ggplot2::xlab("Longitude") + ggplot2::ylab("Latitude") + ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, vjust = 0.5, hjust = 1), legend.text = ggplot2::element_text(size = 8)) + ggplot2::guides(cex = ggplot2::guide_legend(reverse = TRUE))
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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67
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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68 }else{
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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69 mappy <- ggplot2::ggplot(data, ggplot2::aes_string(x = collong, y = collat, cex = colabond, color = colabond)) +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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70 ggplot2::geom_point() + ggplot2::ggtitle(paste("Abundance of", ind, "in the environment")) + ggplot2::xlab("Longitude") + ggplot2::ylab("Latitude") + ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, vjust = 0.5, hjust = 1), legend.text = ggplot2::element_text(size = 8)) + ggplot2::guides(cex = ggplot2::guide_legend(reverse = TRUE))
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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71 }
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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72 ggplot2::ggsave("mappy.png", mappy, width = 20, height = 9, units = "cm")
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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73 }
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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74
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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75 ####Presence absence abundance####
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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76
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77 ## Histogram
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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78 graph_hist <- function(data, col1, col2, col3) {
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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79 cat("\nLocations\n", unique(data[, col1]), file = "Locations.txt", fill = 1, append = TRUE)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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80 if (mult1) {
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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81 for (loc in unique(data[, col1])) {
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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82 data_cut <- data[data[, col1] == loc, ]
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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83 data_cut <- data_cut[data_cut[, col3] > 0, ]
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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84 if (length(unique(data_cut[, col2])) <= 40) {
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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85 top <- nrow(data_cut)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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86 var <- nchar(as.character(round(top * 0.1, digits = 0)))
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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87 step <- round(top * 0.1, digits = ifelse(var == 1, 1, -var + 1))
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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88 graph <- ggplot2::ggplot(data_cut) +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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89 ggplot2::geom_bar(ggplot2::aes_string(x = col1, fill = col2)) +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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90 ggplot2::scale_y_continuous(breaks = seq(from = 0, to = top, by = step)) +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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91 ggplot2::theme(plot.title = ggplot2::element_text(color = "black", size = 12, face = "bold")) +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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92 ggplot2::ggtitle("Number of presence")
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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93
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94 ggplot2::ggsave(paste("number_in_", loc, ".png"), graph)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
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95 }else{
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
96 cat(paste0("\n", loc, " had more than 40 species and plot isn't readable please select a higher taxon level or cut your data"))
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
97 }
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
98 }
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
99 }else{
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
100 top <- nrow(data)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
101 var <- nchar(as.character(round(top * 0.1, digits = 0)))
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
102 step <- round(top * 0.1, digits = ifelse(var == 1, 1, -var + 1))
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
103 graph <- ggplot2::ggplot(data) +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
104 ggplot2::geom_bar(ggplot2::aes_string(x = col1, fill = col2)) +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
105 ggplot2::scale_y_continuous(breaks = seq(from = 0, to = top, by = step)) +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
106 ggplot2::theme(plot.title = ggplot2::element_text(color = "black", size = 12, face = "bold")) +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
107 ggplot2::ggtitle("Number of individuals")
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
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108
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
109 ggplot2::ggsave("number.png", graph)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
110 }
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
111 }
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
112
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
113 rare <- function(data, spe, abond, rare, num) {
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
114 # Put the data in form
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
115 new_data <- as.data.frame(data[, spe])
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
116 colnames(new_data) <- c("Species")
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
117 new_data$total <- data[, abond]
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
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118
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
119 new_data$rarefaction <- as.integer(rare)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
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120
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
121 end <- length(unique(new_data$Species))
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
122 out <- vegan::rarecurve(new_data[, 2:3], step = 10, sample = rarefy_sample, label = FALSE)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
123 names(out) <- paste(unique(new_data$Species), sep = "")
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
124
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
125 # Coerce data into "long" form.
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
126 protox <- mapply(FUN = function(x, y) {
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
127 mydf <- as.data.frame(x)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
128 colnames(mydf) <- "value"
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
129 mydf$species <- y
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
130 mydf$subsample <- attr(x, "Subsample")
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
131 mydf <- na.omit(mydf)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
132 mydf
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
133 }, x = out, y = as.list(names(out)), SIMPLIFY = FALSE)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
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134
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
135 xy <- do.call(rbind, protox)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
136 rownames(xy) <- NULL # pretty
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
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137
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
138 # Plot.
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
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139
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
140 if (mult2) {
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
141 for (spe in unique(data[, spe])) {
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
142 xy_cut <- xy[xy$species == spe, ]
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
143 top <- max(xy_cut$subsample)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
144 var <- nchar(as.character(round(top * 0.1, digits = 0)))
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
145 step <- round(top * 0.1, digits = ifelse(var == 1, 1, -var + 1))
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
146 courbe <- ggplot2::ggplot(xy_cut, ggplot2::aes(x = subsample, y = value)) +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
147 ggplot2::theme_gray() +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
148 ggplot2::geom_line(size = 1) +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
149 ggplot2::scale_x_continuous(breaks = seq(from = 0, to = top, by = step)) +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
150 ggplot2::xlab("Abundance") + ggplot2::ylab("Value") +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
151 ggplot2::ggtitle("rarefaction curve")
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
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152
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
153 ggplot2::ggsave(paste("rarefaction_of_", spe, ".png"), courbe)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
154 }
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
155 }else{
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
156 top <- max(xy$subsample)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
157 var <- nchar(as.character(round(top * 0.1, digits = 0)))
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
158 step <- round(top * 0.1, digits = ifelse(var == 1, 1, -var + 1))
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
159 courbe <- ggplot2::ggplot(xy, ggplot2::aes(x = subsample, y = value, color = species)) +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
160 ggplot2::theme_gray() +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
161 ggplot2::geom_line(size = 1) +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
162 ggplot2::scale_x_continuous(breaks = seq(from = 0, to = top, by = step)) +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
163 ggplot2::xlab("Subsample") + ggplot2::ylab("Value") +
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
164 ggplot2::ggtitle("rarefaction curves")
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
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165
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
166 ggplot2::ggsave("rarefaction.png", courbe)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
167 }
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
168 }
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
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169
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
170 if (abundance) {
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
171 #Maps
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
172 mult0 <- ifelse(length(unique(data[, colspe])) > 10, FALSE, TRUE)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
173 graph_map(data, collong = collong, collat = collat, colabond = colabond, ind = ind, colspe = colspe)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
174 }
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
175
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
176 if (presabs) {
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
177 #Presence absence count
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
178 mult1 <- ifelse(length(unique(data[, colloc])) <= 10, FALSE, TRUE)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
179 graph_hist(data, col1 = colloc, col2 = colspe, col3 = colabond)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
180 }
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
181
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
182 if (rarefaction) {
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
183 #rarefaction
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
184
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
185 #### rarefaction indice ####
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
186 rarefy_sample <- as.numeric(num)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
187
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
188 ## Calcul de la rarefaction
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
189 rarefaction <- vegan::rarefy(data[, abond], rarefy_sample)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
190
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
191 write.table(rarefaction, "rare.tabular")
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
192
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
193 mult2 <- ifelse(length(unique(data[, colspe])) <= 30, FALSE, TRUE)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
194 rare(data, spe = colspe, abond = colabond, rare = rarefaction, num = rarefy_sample)
e5552099d0e3 "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 2f883743403105d9cac6d267496d985100da3958"
ecology
parents:
diff changeset
195 }