Mercurial > repos > ecology > vigiechiro_bilanenrichirp
annotate BilanEnrichiRP.R @ 2:5ad79c210eb9 draft default tip
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro commit 4707473e9991d095310f475a54e041c95accd873
author | ecology |
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date | Wed, 05 Jun 2019 13:48:23 -0400 |
parents | be4e28da3919 |
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be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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1 #!/usr/bin/env Rscript |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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3 args <- commandArgs(trailingOnly = TRUE) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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5 suppressMessages(library(data.table)) |
c55e09a8b4c8
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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6 suppressMessages(library(DT)) |
c55e09a8b4c8
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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7 suppressMessages(library(htmlwidgets)) |
c55e09a8b4c8
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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9 EchelleErreur=c("","POSSIBLE","PROBABLE","SUR") |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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10 EchelleNumErreur=c(99,50,10,1) |
c55e09a8b4c8
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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12 IdC2=fread(args[1],encoding="UTF-8") |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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c55e09a8b4c8
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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c55e09a8b4c8
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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15 if(substr(IdC2$`nom du fichier`[1],2,2)!="i") |
c55e09a8b4c8
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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16 { |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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17 # print("Protocole non conforme, ce script doit etre lance uniquement pour un protocole Routier ou Pedestre") |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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18 print("Wrong protocol, please only use this tool for a \'Pedestre\' or \'Routier\' protocol.") |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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19 }else{ |
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c55e09a8b4c8
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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21 refRP=fread(args[2],encoding="UTF-8") |
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5ad79c210eb9
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro commit 4707473e9991d095310f475a54e041c95accd873
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22 GroupList=fread(args[3],encoding="UTF-8") |
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be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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23 |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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24 IdC2$ConfV[is.na(IdC2$ConfV)]="" |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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25 |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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26 |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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27 Routier=grepl("-",substr(IdC2$`nom du fichier`[1],4,7)) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
ecology
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28 #compute error risk by species (minimum error among files) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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29 #to be replaced by glm outputs if I'll have time |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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30 RisqueErreurT=aggregate(IdC2$IdProb,by=list(IdC2$IdExtrap) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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31 ,FUN=function(x) round((1-max(x))*100)) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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32 barplot(RisqueErreurT$x,names.arg=RisqueErreurT$Group.1,las=2) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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33 #compute error risk accoring to observer/validator (a little dirty because it relies on alphabetical order of confidence classes: POSSIBLE < PROBABLE < SUR) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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34 RisqueErreurOV0=match(IdC2$ConfV,EchelleErreur) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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35 RisqueErreurOV=aggregate(RisqueErreurOV0,by=list(IdC2$IdExtrap) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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36 ,FUN=max) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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37 RisqueErreurOV2=EchelleNumErreur[RisqueErreurOV$x] |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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38 #compute minimum error risk between man and machine |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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39 RisqueErreur=pmin(RisqueErreurT$x,RisqueErreurOV2) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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40 |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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41 #compute number of files validated per species |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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42 FichValid=aggregate(IdC2$IdV,by=list(IdC2$IdExtrap,IdC2$'nom du fichier') |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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43 ,FUN=function(x) sum(x!="")) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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44 NbValid2=aggregate(FichValid$x,by=list(FichValid$Group.1),FUN=function(x) sum(x>0)) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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45 |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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46 DiffC50=vector() # to store the median of confidence difference between unvalidated records and validated ones |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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47 DiffT50=vector() # to store the median of time difference between unvalidated records and validated ones |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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48 for (j in 1:nlevels(as.factor(IdC2$IdExtrap))) |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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49 { |
1
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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50 IdSp=subset(IdC2 |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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51 ,IdC2$IdExtrap==levels(as.factor(IdC2$IdExtrap))[j]) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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52 IdSp$IdProb[is.na(IdSp$IdProb)]=0 |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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53 IdSp=IdSp[order(IdSp$IdProb),] |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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54 IdSpV=subset(IdSp,IdSp$IdV!="") |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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55 if(nrow(IdSpV)>0) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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56 { |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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57 cuts <- c(-Inf, IdSpV$IdProb[-1]-diff(IdSpV$IdProb)/2, Inf) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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58 CorrC=findInterval(IdSp$IdProb, cuts) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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59 CorrC2=IdSpV$IdProb[CorrC] |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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60 DiffC=abs(IdSp$IdProb-CorrC2) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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61 DiffC50=c(DiffC50,median(DiffC)) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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62 |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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63 IdSp=IdSp[order(IdSp$TimeNum),] |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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64 IdSpV=subset(IdSp,IdSp$IdV!="") |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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65 cuts <- c(-Inf, IdSpV$TimeNum[-1]-diff(IdSpV$TimeNum)/2, Inf) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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66 CorrT=findInterval(IdSp$TimeNum, cuts) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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67 CorrT2=IdSpV$TimeNum[CorrT] |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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68 DiffT=abs(IdSp$TimeNum-CorrT2) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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69 DiffT50=c(DiffT50,median(DiffT)) |
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c55e09a8b4c8
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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70 }else{ |
1
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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71 DiffC50=c(DiffC50,Inf) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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72 DiffT50=c(DiffT50,Inf) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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73 } |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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74 } |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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75 #compute an index of validation effort per species |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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76 EffortV=1/DiffC50/DiffT50 |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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77 EffortClass=(EffortV>0.0005)+(EffortV>0.005)+RisqueErreurOV$x |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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78 #cbind(RisqueErreurOV,EffortV,DiffC50,DiffT50) |
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79 barplot(EffortClass-1,names.arg=NbValid2$Group.1,las=2) |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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80 ClassEffortV=c("-","FAIBLE","SUFFISANT","SUFFISANT","FORT","FORT") |
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81 EffortClassMot=ClassEffortV[EffortClass] |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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82 |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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83 |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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84 #compare activity / reference frame |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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85 FileInfo=as.data.table(tstrsplit(IdC2$`nom du fichier`,"-")) |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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86 IdC2$Tron=FileInfo$V4 |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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87 |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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88 MicTempsInfo=as.data.table(tstrsplit(as.data.frame(FileInfo)[,(ncol(FileInfo))],"_")) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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89 MicDroit=(as.data.frame(MicTempsInfo)[,(ncol(MicTempsInfo)-2)]=="1") |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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90 IdC2$MicDroit=MicDroit |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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91 |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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92 testTempsFin=aggregate(IdC2$temps_fin,by=list(MicDroit),FUN=max) |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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93 testTempsFin$Direct=(testTempsFin$x>0.5) |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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94 testTF2=sum((testTempsFin$x>0.5)) |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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95 if(testTF2>1){stop("Probleme stereo : les 2 canaux semblent etre en enregistrement direct")} |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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96 IdC2M=merge(IdC2,testTempsFin,by.x="MicDroit",by.y="Group.1") |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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97 |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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98 ActMoy=aggregate(IdC2$`nom du fichier` |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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99 ,by=list(IdC2M$IdExtrap,IdC2M$Direct),FUN=length) |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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100 ListSpref=match(levels(as.factor(ActMoy$Group.1)),refRP$Espece) |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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101 Subref=refRP[ListSpref] |
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102 if(Routier) |
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103 { |
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104 Subref=Subref[,c(1:17)] |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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105 }else{ |
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106 Subref=Subref[,c(1,18:33)] |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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107 } |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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108 QualifActE=vector() |
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109 QualifActD=vector() |
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110 |
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111 for (k in 1:nlevels(as.factor(ActMoy$Group.1))) |
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112 { |
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113 Actsub=subset(ActMoy,ActMoy$Group.1==levels(as.factor(ActMoy$Group.1))[k]) |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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114 if(is.na(Subref[k,2])) |
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115 { |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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116 QualifActE=c(QualifActE,NA) |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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117 QualifActD=c(QualifActD,NA) |
0
c55e09a8b4c8
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118 }else{ |
1
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119 ActE=subset(Actsub,Actsub$Group.2==F) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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120 if(nrow(ActE)==0) |
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121 { |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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122 QualifActE=c(QualifActE,NA) |
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123 |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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124 }else{ |
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125 cuts=cbind(-Inf,as.numeric(Subref[k,6]),as.numeric(Subref[k,7]) |
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126 ,as.numeric(Subref[k,8]),Inf) |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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127 QualifActE=c(QualifActE,findInterval(ActE$x,cuts,left.open=T)) |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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128 } |
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129 ActD=subset(Actsub,Actsub$Group.2==T) |
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130 if(nrow(ActD)==0) |
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131 { |
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132 QualifActD=c(QualifActD,NA) |
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133 |
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134 }else{ |
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135 cuts=cbind(-Inf,as.numeric(Subref[k,14]),as.numeric(Subref[k,15]) |
be4e28da3919
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136 ,as.numeric(Subref[k,16]),Inf) |
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137 QualifActD=c(QualifActD,findInterval(ActD$x,cuts,left.open=T)) |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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138 } |
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139 |
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140 } |
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141 } |
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142 ClassAct=c("FAIBLE","MODEREE","FORTE","TRES FORTE") |
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143 QualifActMotE=ClassAct[QualifActE] |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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144 QualifActMotD=ClassAct[QualifActD] |
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145 |
1
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146 #compute activity by nights (to be completed) |
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147 #ActNuit=aggregate(IdC2M$`nom du fichier`,by=list(IdC2M$DateNuit,IdC2M$IdExtrap),FUN=length) |
be4e28da3919
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148 ActED=dcast(data=ActMoy,formula=Group.1~Group.2,value=x) |
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149 ActED[is.na(ActED)]=0 |
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150 #organize the csv summary |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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151 SummPart0=cbind(Esp=levels(as.factor(IdC2M$IdExtrap)) |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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152 ,RisqueErreur,NbValid=NbValid2$x,EffortValid=EffortClassMot) |
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153 |
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154 test=match("FALSE",colnames(ActED)) |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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155 if(is.na(test)==F) |
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156 { |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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157 SummPart0=cbind(SummPart0,Contacts_Expansion=ActED$'FALSE' |
be4e28da3919
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
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158 ,Niveau_Activite_Expansion=QualifActMotE) |
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159 }else{ |
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160 SummPart0=cbind(SummPart0,Contacts_Expansion="" |
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161 ,Niveau_Activite_Expansion="") |
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162 } |
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163 test=match("TRUE",colnames(ActED)) |
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164 if(is.na(test)==F) |
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165 { |
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166 |
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167 SummPart0=cbind(SummPart0,Contacts_Direct=ActED$'TRUE' |
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168 ,Niveau_Activite_Direct=QualifActMotD) |
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169 }else{ |
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170 SummPart0=cbind(SummPart0,Contacts_Direct="" |
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171 ,Niveau_Activite_Direct="") |
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172 } |
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173 |
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174 InfoSp=c("GroupFR","NomFR","Scientific name","Esp") |
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175 GroupShort=GroupList[,..InfoSp] |
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176 SummPart=merge(GroupShort,SummPart0,by="Esp") |
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177 IndexGroupe=c("Autre","Sauterelle","Chauve-souris") |
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178 SummPart$IndexSumm=match(SummPart$GroupFR,IndexGroupe) |
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179 SummPart=SummPart[with(SummPart |
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180 ,order(IndexSumm,as.numeric(Contacts_Direct),as.numeric(Contacts_Expansion),decreasing=T)),] |
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181 colnames(SummPart)=c("Code","Groupe","Nom francais","Nom scientifique" |
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182 ,"Risque d'erreur (%)","Nb Validations" |
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183 ,"Effort de validation","Nb de Contacts en expansion" |
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184 ,"Niveau d'Activite en expansion" |
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185 ,"Nb de Contacts en direct" |
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186 ,"Niveau d'Activite en direct","TriGroupe") |
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187 |
1
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188 #to do: extend colors to other columns to improve readability |
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189 SummHTML=datatable(SummPart, rownames = FALSE) %>% |
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190 formatStyle(columns = c("Code","Groupe","Nom francais","Nom scientifique","Risque d'erreur (%)"),valueColumns="Risque d'erreur (%)", |
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191 background = styleInterval(c(1, 10, 50), c("white", "khaki", "orange", "orangered"))) %>% |
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192 formatStyle(columns = "Effort de validation", |
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193 background = styleEqual(c("-","FAIBLE","SUFFISANT","FORT"), c("white", "cyan", "royalblue", "darkblue"))) %>% |
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194 formatStyle(columns = c("Nb de Contacts en expansion","Niveau d'Activite en expansion"),valueColumns="Niveau d'Activite en expansion", |
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195 background = styleEqual(c("FAIBLE","MODEREE","FORTE","TRES FORTE"), c("palegoldenrod", "greenyellow", "limegreen", "darkgreen"))) %>% |
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196 formatStyle(columns = c("Nb de Contacts en direct","Niveau d'Activite en direct"),valueColumns="Niveau d'Activite en direct", |
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197 background = styleEqual(c("FAIBLE","MODEREE","FORTE","TRES FORTE"), c("palegoldenrod", "greenyellow", "limegreen", "darkgreen"))) |
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198 |
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199 |
1
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200 saveWidget(SummHTML,"output-summaryRP.html") |
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201 write.table(SummPart,"output-summaryRP.tabular",row.names=F,sep="\t") |
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202 #write.csv2(SummPart,"output-summaryRP.tabular",row.names=F) #for testing |
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203 |
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204 #summary for each point/transect |
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205 |
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206 #compute number of files validated per species |
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207 IdC2M$Canal=sapply(IdC2M$Direct,FUN=function(x) if(x){"Direct"}else{"Expansion"}) |
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208 |
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209 ActMoyTA=aggregate(IdC2M$`nom du fichier`,by=list(IdC2M$IdExtrap,IdC2M$Canal,IdC2M$Session),FUN=length) |
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210 ActMoyT=dcast(data=IdC2M,formula=IdExtrap+Canal~Session |
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211 ,fun.aggregate=length) |
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212 SummPartshort=cbind(SummPart[,c(1:5)],TriGroupe=SummPart[,TriGroupe]) |
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213 SummPartTron=merge(SummPartshort,ActMoyT,by.x="Code",by.y="IdExtrap") |
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214 SummPartTron=SummPartTron[order(TriGroupe,decreasing=T),] |
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215 |
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216 ListSession=levels(as.factor(IdC2M$Session)) |
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217 brks <- quantile(ActMoyTA$x, probs = seq(.05, .95, .05), na.rm = TRUE)-1 |
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218 clrs <- round(seq(255, 40, length.out = length(brks) + 1), 0) %>% |
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219 {paste0("rgb(255,", ., ",", ., ")")} |
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220 |
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221 |
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222 #to do: extend colors to other columns to improve readability |
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223 SummHTMLT=datatable(SummPartTron, rownames = FALSE) %>% |
0
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224 formatStyle(columns = c("Code","Groupe","Nom francais","Nom scientifique","Risque d'erreur (%)"),valueColumns="Risque d'erreur (%)", |
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225 background = styleInterval(c(1, 10, 50), c("white", "khaki", "orange", "orangered"))) %>% |
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226 formatStyle(columns=ListSession, backgroundColor = styleInterval(brks, clrs)) |
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227 |
1
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228 saveWidget(SummHTMLT,"output-detailRP.html") |
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229 write.table(SummPartTron,"output-detailRP.tabular",row.names=F,sep="\t") |
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230 # write.csv2(SummPartTron,"output-detailRP.tabular",row.names=F)#for testing |
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231 } |