Mercurial > repos > ecology > vigiechiro_idcorrect_2ndlayer
annotate IdCorrect_2ndLayer.R @ 0:6681b6ba1d7e draft
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
author | ecology |
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date | Wed, 13 Mar 2019 11:18:36 -0400 |
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rev | line source |
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6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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1 #!/usr/bin/env Rscript |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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2 |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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3 suppressMessages(library(data.table)) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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4 suppressMessages(library(randomForest)) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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5 args <- commandArgs(trailingOnly = TRUE) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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6 |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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7 set.seed(1) #To test reproductibility |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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8 |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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9 filename=args[3] |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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10 if (exists("ClassifEspC2b")==F){load(args[2])} |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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11 |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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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
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13 DataPar$participation=substr(filename,nchar(filename)-40,nchar(filename)-17) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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14 test1=duplicated(cbind(DataPar$'nom du fichier',DataPar$tadarida_taxon)) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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15 test2=(DataPar$tadarida_taxon=="empty") |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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16 DataPar=subset(DataPar,(!test1)|(test2)) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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17 DataPar$tadarida_probabilite[DataPar$tadarida_probabilite==""]="0" |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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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
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19 |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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20 |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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21 #table counting number of contacts per species |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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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
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23 |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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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
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25 |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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26 #generating input variables for second layer classification |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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27 |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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28 Q25=vector() |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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29 Q50=vector() |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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30 Q75=vector() |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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31 Q90=vector() |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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32 Q95=vector() |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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33 Q98=vector() |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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34 Q100=vector() |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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35 compt=0 |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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36 PropSp=nbcT[0,] |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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37 VoteO=DataPar[0,] |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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38 for (j in 1:nlevels(as.factor(DataPar$tadarida_taxon))) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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39 { |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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40 Datasub2=subset(DataPar,DataPar$tadarida_taxon==levels(as.factor(DataPar$tadarida_taxon))[j]) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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41 |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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42 Q25=c(Q25,rep(quantile(Datasub2$tadarida_probabilite,0.25),nrow(Datasub2))) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
ecology
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43 Q50=c(Q50,rep(quantile(Datasub2$tadarida_probabilite,0.50),nrow(Datasub2))) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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44 Q75=c(Q75,rep(quantile(Datasub2$tadarida_probabilite,0.75),nrow(Datasub2))) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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45 Q90=c(Q90,rep(quantile(Datasub2$tadarida_probabilite,0.90),nrow(Datasub2))) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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46 Q95=c(Q95,rep(quantile(Datasub2$tadarida_probabilite,0.95),nrow(Datasub2))) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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47 Q98=c(Q98,rep(quantile(Datasub2$tadarida_probabilite,0.98),nrow(Datasub2))) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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48 Q100=c(Q100,rep(max(Datasub2$tadarida_probabilite),nrow(Datasub2))) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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49 Ncont1=nrow(Datasub2) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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50 VoteO=rbind(VoteO,Datasub2) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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51 PropSp0=nbcT/Ncont1 |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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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
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53 compt=compt+nrow(Datasub2) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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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
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55 } |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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56 |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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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
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58 |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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59 |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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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
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61 for (i in 15:(ncol(VoteC2)-7)) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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62 { |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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63 colnames(VoteC2)[i]=paste0(names(VoteC2)[i],"_prop") |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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64 } |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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65 |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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66 #Add missing species |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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67 EspForm=subset(row.names(ClassifEspC2b$importance) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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68 ,substr(row.names(ClassifEspC2b$importance) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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69 ,nchar(row.names(ClassifEspC2b$importance))-4 |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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70 ,nchar(row.names(ClassifEspC2b$importance))) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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71 =="_prop") |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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72 test=match(EspForm,colnames(VoteC2)) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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73 EspM=subset(EspForm,is.na(test)) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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74 Zeros=matrix(nrow=nrow(VoteC2),ncol=length(EspM)) |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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75 Zeros[is.na(Zeros)]=0 |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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76 colnames(Zeros)=EspM |
6681b6ba1d7e
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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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
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156 colnames(Zeros)=EspM |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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157 IdS3=cbind(IdS3,Zeros) |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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158 |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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159 #on merge les prop d'espèces, les quantiles et les indices par fichiers et par observations |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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160 #merge species probabilities, quantiles and indice per files and per obs |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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161 VoteC3=merge(VoteC2,MaxI2,by.x="nom du fichier",by.y="V1") |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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162 VoteC4=merge(VoteC3,IdS3,by=c("nom du fichier","tadarida_taxon")) |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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163 VoteC4$temps_fin=as.numeric(as.character(VoteC4$temps_fin)) |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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164 VoteC4$temps_debut=as.numeric(as.character(VoteC4$temps_debut)) |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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165 VoteC4$frequence=as.numeric(as.character(VoteC4$frequence_mediane)) |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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166 VoteC4$durseq=VoteC4$temps_fin-VoteC4$temps_debut |
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167 |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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168 ProbEsp_C2b=predict(ClassifEspC2b,VoteC4,type="prob",norm.votes=TRUE) |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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169 ProbEsp_C2bs=predict(ClassifEspC2b,VoteC4,type="response",norm.votes=TRUE) |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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170 |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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171 colnum=match("participation",colnames(VoteC4)) |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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172 DataCorrC2=cbind(VoteC4[,1:colnum],ProbEsp_C2b,ProbEsp_C2bs) |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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173 DataCorrC2=DataCorrC2[order(DataCorrC2$tadarida_probabilite,decreasing=T),] |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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174 DataCorrC2=DataCorrC2[order(DataCorrC2$'nom du fichier'),] |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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175 |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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176 DataCorrC2$ProbEsp_C2bs=as.character(DataCorrC2$ProbEsp_C2bs) |
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177 DataCorrC2$ProbEsp_C2bs[is.na(DataCorrC2$ProbEsp_C2bs)]="empty" |
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178 |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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179 fout_name="output.tabular" |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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180 |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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181 write.table(DataCorrC2,file=fout_name,row.names=FALSE,sep="\t",quote=FALSE,na="NA") |