comparison FunctTrendSTOCGalaxy.r @ 1:fd0687e91bf6 draft default tip

"planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit d49a4da1ffac1f33a15fdb7ae98827d0034a7879"

0:2e45ae3b297a

    colConserve <- names(which(tabSum>0))
    ## Affichage des espèces rejetees  / show species eliminated for the analyses
    if(length(colNull)>0){
        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="")
        #tabNull <- data.frame(Code_espece = colNull, nom_espece = tabsp[colNull,"nom"])
        #cat("\n\n",sep="")
        tab <- tab[,c("carre","annee",colConserve)]
    }
################################################################################ FIN DE LA PARTIE ISOLABLE
    return(tab)  
}

    ## affichage des especes retirer de l'analyse / print species that will be deleted
    if(length(colSupr)>0){
        cat("\n",length(colSupr)," Rare species removed from the analysis.\n\n",sep="")
        #tabSupr <- subset(tabsp,espece %in% colSupr ,select=c("espece","nom"))
        #tabSupr <- tabSupr[order(tabSupr$espece),]
        #cat("\n\n",sep="")
        
    }
    if(length(colConserve)==0) {
        mess <- "No species available to calculate abundance variation in this dataset."
        stop(mess)

1:fd0687e91bf6

    colConserve <- names(which(tabSum>0))
    ## Affichage des espèces rejetees  / show species eliminated for the analyses
    if(length(colNull)>0){
        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="")
        #tabNull <- data.frame(Code_espece = colNull, nom_espece = tabsp[colNull,"nom"])
        cat("Removed absent species : \n-",paste(colNull,collapse="\n-"),sep="")
        tab <- tab[,c("carre","annee",colConserve)]
    }
################################################################################ FIN DE LA PARTIE ISOLABLE
    return(tab)  
}

    ## affichage des especes retirer de l'analyse / print species that will be deleted
    if(length(colSupr)>0){
        cat("\n",length(colSupr)," Rare species removed from the analysis.\n\n",sep="")
        #tabSupr <- subset(tabsp,espece %in% colSupr ,select=c("espece","nom"))
        #tabSupr <- tabSupr[order(tabSupr$espece),]
        cat("Removed rare species : \n-",paste(colSupr,collapse="\n-"),sep="")
        
    }
    if(length(colConserve)==0) {
        mess <- "No species available to calculate abundance variation in this dataset."
        stop(mess)