Mercurial > repos > ecology > ecoregion_clara_cluster

annotate indval.R @ 7:893b2b010d4a draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
author ecology
date Wed, 23 Jul 2025 14:36:07 +0000
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7
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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1 #Seguineau Pauline
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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2 #02/12/2024
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3 #Indicspecies tool
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4
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5 library(dplyr)
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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6 library(indicspecies)
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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7
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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8 #load arguments
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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9 args = commandArgs(trailingOnly=TRUE)
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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10 if (length(args)==0)
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11 {
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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12 stop("This tool needs at least one argument")
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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13 }else{
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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14 clus_pts <- args[1]
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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15 occ <- args[2]
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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16 spe_name <- args[3]
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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17 sign <- args[4]
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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18 }
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893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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20 ###load data
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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21 clus <- read.table(clus_pts, dec=".", sep="\t", header=T,na.strings = "na") #cluster points file (ecoregionalization workflow)
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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22 data.col <- read.table(occ, dec=".", sep="\t", header=T,na.strings = "na") #occurrence file (merged table from ecoregionalization workflow)
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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23 spe_name = strsplit(spe_name, ",")
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24 spname=NULL
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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26 for (n in spe_name) {
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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27 spname = cbind(names(data.col[as.numeric(n)]))}
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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29 #Rename decimalLatitude and decimalLongitude columns from occurrence file
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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30 if ("decimalLatitude" %in% colnames(data.col)) {
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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31 colnames(data.col)[which(colnames(data.col) == "decimalLatitude")] <- "lat"
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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32 }
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33 if ("decimalLongitude" %in% colnames(data.col)) {
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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34 colnames(data.col)[which(colnames(data.col) == "decimalLongitude")] <- "long"
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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35 }
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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37 #Round lat and long of the data.col file to be able to put clus cluster in it
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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38 data.col$lat = round(data.col$lat,digits = 2)
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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39 data.col$long = round(data.col$long,digits = 2)
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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41 # Creates a new "station" column that associates a unique identifier to each latitude-longitude pair
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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42 data.col <- data.col %>% mutate(station = as.factor(paste(lat, long, sep = "_")))
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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44 # convert "station" to a unique numeric identifier
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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45 data.col <- data.col %>% mutate(station = as.numeric(factor(station)))
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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47 #Adding clusters to file
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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48 clusta <- merge(data.col,clus, by=c("lat","long"), all.x = TRUE)
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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49
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50 #This generated duplicates with different clusters
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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51 clusta <- aggregate(clusta, by=list(clusta$station,clusta$cluster), FUN=mean, na.rm=TRUE)
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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52 clusta <- na.exclude(clusta)
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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54 # indval on all clusters
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55 indval = multipatt(clusta[,spname], clusta$cluster,duleg = TRUE, control = how(nperm=999))
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56 if (sign=="true"){
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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57 capture.output(summary(indval,indvalcomp=TRUE), file = "indval.txt")
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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58 }else{
893b2b010d4a planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
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59 capture.output(summary(indval,indvalcomp=TRUE, alpha=1), file = "indval.txt")}