Mercurial > repos > ecology > ecoregion_cluster_estimate

annotate indval.R @ 7:8307fa98be22 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/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
author ecology
date Wed, 23 Jul 2025 14:37:26 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
1 #Seguineau Pauline
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
2 #02/12/2024
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
3 #Indicspecies tool
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
4
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
5 library(dplyr)
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
6 library(indicspecies)
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
7
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
8 #load arguments
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
9 args = commandArgs(trailingOnly=TRUE)
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
10 if (length(args)==0)
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
11 {
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
12 stop("This tool needs at least one argument")
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
13 }else{
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
14 clus_pts <- args[1]
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
15 occ <- args[2]
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
16 spe_name <- args[3]
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
17 sign <- args[4]
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
18 }
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
19
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
20 ###load data
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
21 clus <- read.table(clus_pts, dec=".", sep="\t", header=T,na.strings = "na") #cluster points file (ecoregionalization workflow)
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
22 data.col <- read.table(occ, dec=".", sep="\t", header=T,na.strings = "na") #occurrence file (merged table from ecoregionalization workflow)
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
23 spe_name = strsplit(spe_name, ",")
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
24 spname=NULL
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
25
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
26 for (n in spe_name) {
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
27 spname = cbind(names(data.col[as.numeric(n)]))}
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
28
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
29 #Rename decimalLatitude and decimalLongitude columns from occurrence file
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
30 if ("decimalLatitude" %in% colnames(data.col)) {
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
31 colnames(data.col)[which(colnames(data.col) == "decimalLatitude")] <- "lat"
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
32 }
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
33 if ("decimalLongitude" %in% colnames(data.col)) {
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
34 colnames(data.col)[which(colnames(data.col) == "decimalLongitude")] <- "long"
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
35 }
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
36
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
37 #Round lat and long of the data.col file to be able to put clus cluster in it
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
38 data.col$lat = round(data.col$lat,digits = 2)
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
39 data.col$long = round(data.col$long,digits = 2)
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
40
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
41 # Creates a new "station" column that associates a unique identifier to each latitude-longitude pair
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
42 data.col <- data.col %>% mutate(station = as.factor(paste(lat, long, sep = "_")))
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
43
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
44 # convert "station" to a unique numeric identifier
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
45 data.col <- data.col %>% mutate(station = as.numeric(factor(station)))
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
46
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
47 #Adding clusters to file
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
48 clusta <- merge(data.col,clus, by=c("lat","long"), all.x = TRUE)
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
49
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
50 #This generated duplicates with different clusters
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
51 clusta <- aggregate(clusta, by=list(clusta$station,clusta$cluster), FUN=mean, na.rm=TRUE)
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
52 clusta <- na.exclude(clusta)
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
53
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
54 # indval on all clusters
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
55 indval = multipatt(clusta[,spname], clusta$cluster,duleg = TRUE, control = how(nperm=999))
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
56 if (sign=="true"){
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
57 capture.output(summary(indval,indvalcomp=TRUE), file = "indval.txt")
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
58 }else{
8307fa98be22 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 9dee19b2d28b61a81f2a89d4c7d35678e31a9927
ecology
parents:
diff changeset
59 capture.output(summary(indval,indvalcomp=TRUE, alpha=1), file = "indval.txt")}