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annotate Moyenne_geom.r @ 0:ce9979488ebb draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
author ecology
date Sat, 25 Nov 2023 15:18:33 +0000
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ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
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1 #### loading required R libraries
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
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2 #### chargement des packages R utilisés
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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3 library(gdata)
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
ecology
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4 library(XLConnect)
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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5 library(rms)
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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7 ###### overall parameters and settings
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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8 ###### paramètres globaux utilisés
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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10 args = commandArgs(trailingOnly=TRUE)
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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11 if (length(args)==0)
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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12 {
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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13 stop("This tool needs at least one argument")
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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14 }else{
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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15 data <- args[1]
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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16 sep <- args[2]
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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17 HR <- args[3]
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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19 }
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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21 if (HR =="false"){HR<-FALSE} else {HR<-TRUE}
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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23 ###nrep: number of samples used to calculate geometric means
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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24 ###nrep: nombre d'échantillons utilisés pour calculer les moyennes géométriques
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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25 nrep<-10000
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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27 #______________________________________________________________________________________________________________________________________________________________________________________________
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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28 ###### common functions
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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29 ###### fonction utiles pour la suite
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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31 convert.to.numeric<-function(x){
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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32 t(apply(x,1,function(x){as.double(sub(" ","",as.character(x)))}))}
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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35 ### calculus of the logarithm of nrep geometric means, sampling based on a lognormal distribution with the same moments as the empirical ones (means & Ics)
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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36 #to prevent negative values
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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37 ### calcul du logarithme de nrep moyennes géométriques, l'échantillonnage étant fait avec la distribution lognormale de mêmes moments que les momenst empriques (means et ICs)
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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38 #pour éviter d'avoir des valeurs négatives
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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40 lgeomean<-function(means,ICs,nrep)
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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41 {#means: vector: mean estimates for the different categories
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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42 #ICs: vector: in proportion to the mean, difference between the extremum of the 95% confidence interval and the mean
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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43 require(mvtnorm)
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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44 #calculation of the parameters of the log normal distribution (on the log scale)
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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45 #cf. http://127.0.0.1:26338/library/stats/html/Lognormal.html
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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46 logsigma<-sqrt(log((ICs/qnorm(0.975)/means)^2+1))
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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47 logmean<-log(means)-1/2*logsigma^2
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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48
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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49 #gaussian sampling on the log scale then taking exponential
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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50 temp<-exp(rmvnorm(nrep,mean=logmean,sigma=diag(logsigma*logsigma)))
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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52 #taking geometric mean over categories, but kept on the log scale
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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53 geomm.rep<-apply(temp,1,function(x){(mean(log(x),na.rm=TRUE))})
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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54 #c(mean(geomm.rep),sd(geomm.rep))
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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55 geomm.rep}
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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56 #_______________________________________________________________________________________________________________________________________________________________________________________________
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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58 ###### importation des données
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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59 ###### importation of data
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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60 temp<-read.csv(file=data,sep=sep,header=HR,encoding="UTF-8")
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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62 data2008_2012<-temp[4:14,]
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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63 data2013_2017<-temp[21:31,]
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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65 meandata2008_2012<-convert.to.numeric(data2008_2012[,c(3,6,9)])
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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66 ICdata2008_2012<-convert.to.numeric(data2008_2012[,c(5,8,11)])
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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67 meandata2013_2017<-convert.to.numeric(data2013_2017[,c(3,6,9)])
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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68 ICdata2013_2017<-convert.to.numeric(data2013_2017[,c(5,8,11)])
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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70 ####### code to calculate (nrep) logarithms of geometric means by region (Greco)
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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71 ####### code pour calculer les nrep logarithmes de moyennes géométriques par région (GRECO)
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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73 set.seed(1)
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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74 #first period
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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75 #première période
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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76 rest2008_2012<-sapply(1:dim(data2008_2012)[1],function(region){lgeomean(meandata2008_2012[region,],ICdata2008_2012[region,],nrep)})
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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78 set.seed(3)
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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79 #first period but with different seed
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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80 #première période mais avec une graine différente
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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81 rest2008_2012_s3<-sapply(1:dim(data2008_2012)[1],function(region){lgeomean(meandata2008_2012[region,],ICdata2008_2012[region,],nrep)})
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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83 set.seed(2)
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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84 #second period
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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85 #seconde période
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86 rest2013_2017<-sapply(1:dim(data2013_2017)[1],function(region){lgeomean(meandata2013_2017[region,],ICdata2013_2017[region,],nrep)})
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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87
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88
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89 ####### code to summarize the above nrep logarithms of geometric means by region into the statistics of an overall geometric mean across regions, taking the first period as reference
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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90 ###### code pour passer des nrep logarithmes de moyenne géométrique par région aux statistiques de la moyenne géométrique globale, en prennat la première période comme référence
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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91
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92 #for the first period
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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93 #pour la première période
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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94 Mean_2008_2012_scaled<-{temp<-apply(rest2008_2012_s3,1,function(x){mean(x)})-apply(rest2008_2012,1,function(x){mean(x)});c(mean(exp(temp)),sd(exp(temp)),quantile(exp(temp),prob=c(0.025,0.975)))}
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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95
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96 #for the second period
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97 #pour la seconde période
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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98 Mean_2013_2017_scaled<-{temp<-apply(rest2013_2017,1,function(x){mean(x)})-apply(rest2008_2012,1,function(x){mean(x)});c(mean(exp(temp)),sd(exp(temp)),quantile(exp(temp),prob=c(0.025,0.975)))}
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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99
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100
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101
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102 ############### NATIONAL OUPUTS:
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103 ############### SORTIES NATIONALES:
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104
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105 res2008_2012_scaled_df = data.frame(Mean_2008_2012_scaled)
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106 res2008_2012_scaled_df=`rownames<-`(res2008_2012_scaled_df,c("mean","sd","2,5%","97,5%"))
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107
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108 res2013_2017_scaled_df = data.frame(Mean_2013_2017_scaled)
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109 res2013_2017_scaled_df=`rownames<-`(res2013_2017_scaled_df,c("mean","sd","2,5%","97,5%"))
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110
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111
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112 write.csv(res2008_2012_scaled_df, file = "res2008_2012_scaled.csv")
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113 write.csv(res2013_2017_scaled_df,file= "res2013_2017_scaled.csv")
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114
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115 ############### REGIONAL OUPUTS:
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116 ############### SORTIES REGIONALES (GRECO):
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117
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118 regres2008_2012_scaled<-apply(rest2008_2012_s3-rest2008_2012,2,function(x){temp<-x;c(mean=mean(exp(temp)),sd=sd(exp(temp)),quantile(exp(temp),prob=c(0.025,0.975)))})
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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119 regres2013_2017_scaled<-apply(rest2013_2017-rest2008_2012,2,function(x){temp<-x;c(mean=mean(exp(temp)),sd=sd(exp(temp)),quantile(exp(temp),prob=c(0.025,0.975)))})
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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120 dimnames(regres2008_2012_scaled)[[2]]<-as.character(data2008_2012[,2])
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121 dimnames(regres2013_2017_scaled)[[2]]<-as.character(data2013_2017[,2])
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122
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123 write.csv(regres2008_2012_scaled, file = "regres2008_2012_scaled.csv")
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124 write.csv(regres2013_2017_scaled, file = "regres2013_2017_scaled.csv")
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125
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126 ############### data to make a bar plot of the national evolution rate
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127 histo_data = data.frame(
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128 variable_name = c(names(res2008_2012_scaled_df),names(res2013_2017_scaled_df)),
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129 variable = c(round(Mean_2008_2012_scaled[1]*100),round(Mean_2013_2017_scaled[1]*100)),
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130 standard_deviation = c(Mean_2008_2012_scaled[2]*100,Mean_2013_2017_scaled[2]*100)
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131 )
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132
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133 write.table(histo_data, file = "histo_data.tsv",row.names = F, col.names = T ,sep ="\t")
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134
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135 ############### data to make a map of the GRECO evolution rate
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136
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137 rate2008_2012 = data.frame(round(regres2008_2012_scaled[1,1:11]*100))
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138 rate2013_2017 = data.frame(round(regres2013_2017_scaled[1,1:11]*100))
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139
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140 evol_rate = rate2013_2017-rate2008_2012
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141 evol_rate = cbind(data2013_2017[,2],evol_rate)
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142 colnames(evol_rate)<-c("Regions","Evolution_rate")
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143
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145 write.table(evol_rate,"evolution_rate.tsv",sep="\t",quote=F,row.names=F,col.names=T)
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