Mercurial > repos > ecology > stoc_filteringsp

comparison FunctTrendSTOCGalaxy.r @ 1:fd0687e91bf6 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit d49a4da1ffac1f33a15fdb7ae98827d0034a7879"
author ecology
date Mon, 11 May 2020 17:44:48 -0400
parents 2e45ae3b297a
children
comparison
equal deleted inserted replaced
0:2e45ae3b297a 1:fd0687e91bf6
60 colConserve <- names(which(tabSum>0)) 60 colConserve <- names(which(tabSum>0))
61 ## Affichage des espèces rejetees / show species eliminated for the analyses 61 ## Affichage des espèces rejetees / show species eliminated for the analyses
62 if(length(colNull)>0){ 62 if(length(colNull)>0){
63 cat("\n",length(colNull)," Species removed from the analysis, abundance is always 0.\n\n",sep="") #Espèces enlevées de l'analyse car abondance toujours égale a 0\n\n",sep="") 63 cat("\n",length(colNull)," Species removed from the analysis, abundance is always 0.\n\n",sep="") #Espèces enlevées de l'analyse car abondance toujours égale a 0\n\n",sep="")
64 #tabNull <- data.frame(Code_espece = colNull, nom_espece = tabsp[colNull,"nom"]) 64 #tabNull <- data.frame(Code_espece = colNull, nom_espece = tabsp[colNull,"nom"])
65 #cat("\n\n",sep="") 65 cat("Removed absent species : \n-",paste(colNull,collapse="\n-"),sep="")
66 tab <- tab[,c("carre","annee",colConserve)] 66 tab <- tab[,c("carre","annee",colConserve)]
67 } 67 }
68 ################################################################################ FIN DE LA PARTIE ISOLABLE 68 ################################################################################ FIN DE LA PARTIE ISOLABLE
69 return(tab) 69 return(tab)
70 } 70 }
117 ## affichage des especes retirer de l'analyse / print species that will be deleted 117 ## affichage des especes retirer de l'analyse / print species that will be deleted
118 if(length(colSupr)>0){ 118 if(length(colSupr)>0){
119 cat("\n",length(colSupr)," Rare species removed from the analysis.\n\n",sep="") 119 cat("\n",length(colSupr)," Rare species removed from the analysis.\n\n",sep="")
120 #tabSupr <- subset(tabsp,espece %in% colSupr ,select=c("espece","nom")) 120 #tabSupr <- subset(tabsp,espece %in% colSupr ,select=c("espece","nom"))
121 #tabSupr <- tabSupr[order(tabSupr$espece),] 121 #tabSupr <- tabSupr[order(tabSupr$espece),]
122 #cat("\n\n",sep="") 122 cat("Removed rare species : \n-",paste(colSupr,collapse="\n-"),sep="")
123 123
124 } 124 }
125 if(length(colConserve)==0) { 125 if(length(colConserve)==0) {
126 mess <- "No species available to calculate abundance variation in this dataset." 126 mess <- "No species available to calculate abundance variation in this dataset."
127 stop(mess) 127 stop(mess)