Mercurial > repos > ecology > vigiechiro_idcorrect_2ndlayer

annotate IdCorrect_2ndLayer.R @ 0:6681b6ba1d7e draft

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/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
author ecology
date Wed, 13 Mar 2019 11:18:36 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
1 #!/usr/bin/env Rscript
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
2
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
3 suppressMessages(library(data.table))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
4 suppressMessages(library(randomForest))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
5 args <- commandArgs(trailingOnly = TRUE)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
6
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
7 set.seed(1) #To test reproductibility
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
8
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
9 filename=args[3]
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
10 if (exists("ClassifEspC2b")==F){load(args[2])}
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
11
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
12 DataPar=fread(args[1],na.strings="") #id to be corrected
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
13 DataPar$participation=substr(filename,nchar(filename)-40,nchar(filename)-17)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
14 test1=duplicated(cbind(DataPar$'nom du fichier',DataPar$tadarida_taxon))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
15 test2=(DataPar$tadarida_taxon=="empty")
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
16 DataPar=subset(DataPar,(!test1)|(test2))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
17 DataPar$tadarida_probabilite[DataPar$tadarida_probabilite==""]="0"
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
18 DataPar$tadarida_probabilite=as.numeric(DataPar$tadarida_probabilite)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
19
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
20
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
21 #table counting number of contacts per species
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
22 nbcT=as.matrix(table(DataPar$participation,DataPar$tadarida_taxon))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
23
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
24 DataPar$tadarida_probabilite=as.numeric(DataPar$tadarida_probabilite)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
25
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
26 #generating input variables for second layer classification
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
27
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
28 Q25=vector()
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
29 Q50=vector()
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
30 Q75=vector()
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
31 Q90=vector()
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
32 Q95=vector()
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
33 Q98=vector()
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
34 Q100=vector()
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
35 compt=0
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
36 PropSp=nbcT[0,]
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
37 VoteO=DataPar[0,]
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
38 for (j in 1:nlevels(as.factor(DataPar$tadarida_taxon)))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
39 {
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
40 Datasub2=subset(DataPar,DataPar$tadarida_taxon==levels(as.factor(DataPar$tadarida_taxon))[j])
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
41
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
42 Q25=c(Q25,rep(quantile(Datasub2$tadarida_probabilite,0.25),nrow(Datasub2)))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
43 Q50=c(Q50,rep(quantile(Datasub2$tadarida_probabilite,0.50),nrow(Datasub2)))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
44 Q75=c(Q75,rep(quantile(Datasub2$tadarida_probabilite,0.75),nrow(Datasub2)))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
45 Q90=c(Q90,rep(quantile(Datasub2$tadarida_probabilite,0.90),nrow(Datasub2)))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
46 Q95=c(Q95,rep(quantile(Datasub2$tadarida_probabilite,0.95),nrow(Datasub2)))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
47 Q98=c(Q98,rep(quantile(Datasub2$tadarida_probabilite,0.98),nrow(Datasub2)))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
48 Q100=c(Q100,rep(max(Datasub2$tadarida_probabilite),nrow(Datasub2)))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
49 Ncont1=nrow(Datasub2)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
50 VoteO=rbind(VoteO,Datasub2)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
51 PropSp0=nbcT/Ncont1
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
52 PropSp=rbind(PropSp,PropSp0[rep(seq_len(nrow(PropSp0)),nrow(Datasub2)),])
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
53 compt=compt+nrow(Datasub2)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
54 #print(paste(compt,levels(as.factor(DataPar$tadarida_taxon))[j]))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
55 }
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
56
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
57 VoteC2=cbind(VoteO,PropSp,Q25,Q50,Q75,Q90,Q95,Q98,Q100)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
58
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
59
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
60 #editing column titles to identify var of type "proportion d'abondances"
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
61 for (i in 15:(ncol(VoteC2)-7))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
62 {
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
63 colnames(VoteC2)[i]=paste0(names(VoteC2)[i],"_prop")
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
64 }
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
65
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
66 #Add missing species
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
67 EspForm=subset(row.names(ClassifEspC2b$importance)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
68 ,substr(row.names(ClassifEspC2b$importance)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
69 ,nchar(row.names(ClassifEspC2b$importance))-4
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
70 ,nchar(row.names(ClassifEspC2b$importance)))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
71 =="_prop")
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
72 test=match(EspForm,colnames(VoteC2))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
73 EspM=subset(EspForm,is.na(test))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
74 Zeros=matrix(nrow=nrow(VoteC2),ncol=length(EspM))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
75 Zeros[is.na(Zeros)]=0
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
76 colnames(Zeros)=EspM
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
77 VoteC2=cbind(VoteC2,Zeros)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
78
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
79 ListDV=levels(as.factor(DataPar$'nom du fichier'))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
80 #calcule les probabilités max par espèce et par fichier
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
81 #(utile pour corriger les erreurs dues à la coexistence de taxons dans le même fichier
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
82 #ex: cris sociaux de Pipistrelles identifiées comme autre chose (Noctule, oreillard...))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
83 #comptue max proba per species and files
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
84 #(useful to correct errors that came from multiple taxons in the same file
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
85 #eg ; Pipistrelles socials shouting identified as something else (Noctule, oreillard..))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
86
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
87 MaxI=tapply(DataPar$tadarida_probabilite
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
88 ,INDEX=list(c(DataPar$'nom du fichier'),c(DataPar$tadarida_taxon))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
89 ,FUN=max)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
90 MaxI2=as.data.frame(cbind(row.names(MaxI),MaxI))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
91 for (i in 2:ncol(MaxI2))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
92 {
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
93 MaxI2[,i]=as.numeric(as.character(MaxI2[,i]))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
94 }
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
95 MaxI2[is.na(MaxI2)]=0
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
96
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
97 #édition des titres de colonne pour identifier les variables de type "indices max"
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
98 #editing col titles to identify "indices max" variables
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
99 for (i in 2:(ncol(MaxI2)))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
100 {
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
101 colnames(MaxI2)[i]=paste0(names(MaxI2)[i],"_maxI")
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
102 }
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
103
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
104
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
105 #add missing species
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
106 EspForm=subset(row.names(ClassifEspC2b$importance)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
107 ,substr(row.names(ClassifEspC2b$importance)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
108 ,nchar(row.names(ClassifEspC2b$importance))-4
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
109 ,nchar(row.names(ClassifEspC2b$importance)))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
110 =="_maxI")
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
111 test=match(EspForm,colnames(MaxI2))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
112 EspM=subset(EspForm,is.na(test))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
113 Zeros=matrix(nrow=nrow(MaxI2),ncol=length(EspM))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
114 Zeros[is.na(Zeros)]=0
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
115 colnames(Zeros)=EspM
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
116 MaxI2=cbind(MaxI2,Zeros)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
117
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
118
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
119
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
120
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
121 #indice de confiance à l'echelle de l'observation (groupe de cris identifié comme provenant d'une seule espèce par la première couche)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
122 #Confidence indice on obs scale (shoutings groups identified as comming from a single species from the first layer)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
123 if(exists("IdS3")){rm(IdS3)}
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
124 for (i in 1:nlevels(as.factor(DataPar$tadarida_taxon)))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
125 {
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
126 Idsub=subset(DataPar,DataPar$tadarida_taxon==levels(as.factor(DataPar$tadarida_taxon))[i])
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
127 IdS2=cbind('nom du fichier'=Idsub$'nom du fichier',tadarida_taxon=Idsub$tadarida_taxon,prob=Idsub$tadarida_probabilite)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
128 colnames(IdS2)[3]=paste(levels(as.factor(DataPar$tadarida_taxon))[i])
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
129 if(exists("IdS3")){IdS3=merge(IdS3,IdS2,all=T)}else{IdS3=IdS2}
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
130 }
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
131
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
132 for (i in 3:ncol(IdS3))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
133 {
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
134 IdS3[,i]=as.numeric(as.character(IdS3[,i]))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
135 }
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
136
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
137 #édition des titres de colonne pour identifier les variables de type "indices de l'observation"
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
138 #editing col titles to identify "indices de l'observation" variables
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
139 for (i in 3:(ncol(IdS3)))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
140 {
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
141 colnames(IdS3)[i]=paste0(names(IdS3)[i],"_ValI")
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
142 }
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
143
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
144 IdS3[is.na(IdS3)]=0
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
145
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
146 #add missing species
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
147 EspForm=subset(row.names(ClassifEspC2b$importance)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
148 ,substr(row.names(ClassifEspC2b$importance)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
149 ,nchar(row.names(ClassifEspC2b$importance))-4
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
150 ,nchar(row.names(ClassifEspC2b$importance)))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
151 =="_ValI")
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
152 test=match(EspForm,colnames(IdS3))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
153 EspM=subset(EspForm,is.na(test))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
154 Zeros=matrix(nrow=nrow(IdS3),ncol=length(EspM))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
155 Zeros[is.na(Zeros)]=0
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
156 colnames(Zeros)=EspM
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
157 IdS3=cbind(IdS3,Zeros)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
158
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
159 #on merge les prop d'espèces, les quantiles et les indices par fichiers et par observations
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
160 #merge species probabilities, quantiles and indice per files and per obs
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
161 VoteC3=merge(VoteC2,MaxI2,by.x="nom du fichier",by.y="V1")
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
162 VoteC4=merge(VoteC3,IdS3,by=c("nom du fichier","tadarida_taxon"))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
163 VoteC4$temps_fin=as.numeric(as.character(VoteC4$temps_fin))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
164 VoteC4$temps_debut=as.numeric(as.character(VoteC4$temps_debut))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
165 VoteC4$frequence=as.numeric(as.character(VoteC4$frequence_mediane))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
166 VoteC4$durseq=VoteC4$temps_fin-VoteC4$temps_debut
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
167
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
168 ProbEsp_C2b=predict(ClassifEspC2b,VoteC4,type="prob",norm.votes=TRUE)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
169 ProbEsp_C2bs=predict(ClassifEspC2b,VoteC4,type="response",norm.votes=TRUE)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
170
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
171 colnum=match("participation",colnames(VoteC4))
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
172 DataCorrC2=cbind(VoteC4[,1:colnum],ProbEsp_C2b,ProbEsp_C2bs)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
173 DataCorrC2=DataCorrC2[order(DataCorrC2$tadarida_probabilite,decreasing=T),]
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
174 DataCorrC2=DataCorrC2[order(DataCorrC2$'nom du fichier'),]
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
175
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
176 DataCorrC2$ProbEsp_C2bs=as.character(DataCorrC2$ProbEsp_C2bs)
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
177 DataCorrC2$ProbEsp_C2bs[is.na(DataCorrC2$ProbEsp_C2bs)]="empty"
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
178
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
179 fout_name="output.tabular"
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
180
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
parents:
diff changeset
181 write.table(DataCorrC2,file=fout_name,row.names=FALSE,sep="\t",quote=FALSE,na="NA")