Mercurial > repos > mnhn65mo > vigiechiro
changeset 0:0e3db3a308c0 draft default tip
Uploaded
| author | mnhn65mo |
|---|---|
| date | Mon, 06 Aug 2018 09:13:29 -0400 |
| parents | |
| children | |
| files | BilanEnrichiPF.R BilanEnrichiPFen.xml BilanEnrichiRP.R BilanEnrichiRPen.xml ClassifEspC2b_180222.learner GroupList_HF.csv IdCorrect_2ndLayer.R IdCorrect_2ndLayer_en.xml IdValid.R IdValiden.xml Referentiel_seuils_C2.csv SpeciesList.csv refPF.csv refRPSeuil50.csv |
| diffstat | 14 files changed, 1695 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BilanEnrichiPF.R Mon Aug 06 09:13:29 2018 -0400 @@ -0,0 +1,249 @@ +library(data.table) +library(DT) +library(htmlwidgets) + +f2p <- function(x) #get date-time data from recording file names +{ + if (is.data.frame((x)[1])) {pretemps <- vector(length = nrow(x))} + op <- options(digits.secs = 3) + pretemps <- paste(substr(x, nchar(x) - 18, nchar(x)-4), ".", substr(x, nchar(x) - 2, nchar(x)), sep = "") + strptime(pretemps, "%Y%m%d_%H%M%OS",tz="UTC")-7200 +} + +args <- commandArgs(trailingOnly = TRUE) +#print(args) +EchelleErreur=c("","POSSIBLE","PROBABLE","SUR") +EchelleNumErreur=c(99,50,10,1) + +#for test +#inputest=list.files("C:/Users/Yves Bas/Documents/GitHub/65MO_Galaxy-E/raw_scripts/Vigie-Chiro/output_IdValid_input_BilanEnrichi/",pattern="IdC2.csv",full.names=T) +#for (i in 1:length(inputest)) +#{ +# args=c(inputest[i],"refPF.csv","SpeciesList.csv") + + +IdC2=fread(args[1]) +refPF=fread(args[2]) +GroupList=fread(args[3]) + +if(substr(IdC2$`nom du fichier`[1],2,2)!="a") +{ + print("Protocole non conforme, ce script doit etre lance pour un protocole Point Fixe") +}else{ + + +#compute error risk by species (minimum error among files) +#to be replaced by glm outputs if I'll have time +RisqueErreurT=aggregate(IdC2$IdProb,by=list(IdC2$IdExtrap),FUN=function(x) ceiling((1-max(x-0.0001))*100)) +barplot(RisqueErreurT$x,names.arg=RisqueErreurT$Group.1,las=2) +#compute error risk accoring to observer/validator (a little dirty because it relies on alphabetical order of confidence classes: POSSIBLE < PROBABLE < SUR) +RisqueErreurOV0=match(IdC2$ConfV,EchelleErreur) +RisqueErreurOV=aggregate(RisqueErreurOV0,by=list(IdC2$IdExtrap) + ,FUN=max) +RisqueErreurOV2=EchelleNumErreur[RisqueErreurOV$x] +#compute minimum error risk between man and machine +RisqueErreur=pmin(RisqueErreurT$x,RisqueErreurOV2) + +#compute number of files validated per species +FichValid=aggregate(IdC2$IdV,by=list(IdC2$IdExtrap,IdC2$'nom du fichier') + ,FUN=function(x) sum(x!="")) +NbValid2=aggregate(FichValid$x,by=list(FichValid$Group.1),FUN=function(x) sum(x>0)) + +DiffC50=vector() # to store the median of confidence difference between unvalidated records and validated ones +DiffT50=vector() # to store the median of time difference between unvalidated records and validated ones +for (j in 1:nlevels(as.factor(IdC2$IdExtrap))) +{ + IdSp=subset(IdC2 + ,IdC2$IdExtrap==levels(as.factor(IdC2$IdExtrap))[j]) + IdSp=IdSp[order(IdSp$IdProb),] + IdSpV=subset(IdSp,IdSp$IdV!="") + if(nrow(IdSpV)>0) + { + cuts <- c(-Inf, IdSpV$IdProb[-1]-diff(IdSpV$IdProb)/2, Inf) + CorrC=findInterval(IdSp$IdProb, cuts) + CorrC2=IdSpV$IdProb[CorrC] + DiffC=abs(IdSp$IdProb-CorrC2) + DiffC50=c(DiffC50,median(DiffC)) + + IdSp=IdSp[order(IdSp$TimeNum),] + IdSpV=subset(IdSp,IdSp$IdV!="") + cuts <- c(-Inf, IdSpV$TimeNum[-1]-diff(IdSpV$TimeNum)/2, Inf) + CorrT=findInterval(IdSp$TimeNum, cuts) + CorrT2=IdSpV$TimeNum[CorrT] + DiffT=abs(IdSp$TimeNum-CorrT2) + DiffT50=c(DiffT50,median(DiffT)) + }else{ + DiffC50=c(DiffC50,Inf) + DiffT50=c(DiffT50,Inf) + } +} +#compute an index of validation effort per species +EffortV=1/DiffC50/DiffT50 +EffortClass=(EffortV>0.0005)+(EffortV>0.005)+RisqueErreurOV$x +cbind(RisqueErreurOV,EffortV,DiffC50,DiffT50) +barplot(EffortClass-1,names.arg=NbValid2$Group.1,las=2) +ClassEffortV=c("-","FAIBLE","SUFFISANT","SUFFISANT","FORT","FORT") +EffortClassMot=ClassEffortV[EffortClass] + + +#get date-night +pourDateNuit=IdC2$TimeNum-12*3600 #bricolage-decalage de 12 heures pour ramener a la date du debut de nuit +DateNuit=as.Date.POSIXct(pourDateNuit) # date of the beginning of the night +DateJour=as.Date.POSIXct(IdC2$TimeNum) # date (UTC+0) +IdC2$DateNuit=DateNuit +IdC2$DateJour=DateJour +NbNuit=as.numeric(max(IdC2$DateNuit)-min(IdC2$DateNuit))+1 + +#compare activity / reference frame +ActMoy=aggregate(IdC2$`nom du fichier` + ,by=list(IdC2$IdExtrap),FUN=function(x) length(x)/NbNuit) +ListSpref=match(ActMoy$Group.1,refPF$Espece) +Subref=refPF[ListSpref] +QualifAct=vector() +for (k in 1:nrow(ActMoy)) +{ + if(is.na(Subref$Q25[k])) + { + QualifAct=c(QualifAct,NA) + }else{ + cuts=cbind(-Inf,as.numeric(Subref$Q25[k]),as.numeric(Subref$Q75[k]) + ,as.numeric(Subref$Q98[k]),Inf) + + QualifAct=c(QualifAct,findInterval(ActMoy$x[k],cuts,left.open=T)) + } +} +ClassAct=c("FAIBLE","MODEREE","FORTE","TRES FORTE") +QualifActMot=ClassAct[QualifAct] + +#compute activity by nights (to be completed) +#ActNuit=aggregate(IdC2$`nom du fichier`,by=list(IdC2$DateNuit,IdC2$IdExtrap),FUN=length) + +#organize the csv summary +SummPart0=cbind(Esp=levels(as.factor(IdC2$IdExtrap)) + ,RisqueErreur,NbValid=NbValid2$x,EffortValid=EffortClassMot + ,Contacts_Nuit=round(ActMoy$x),Niveau_Activite=QualifActMot) + + +InfoSp=c("GroupFR","NomFR","Scientific name","Esp") +GroupShort=GroupList[,InfoSp,with=FALSE] +#GroupShort=GroupList[,..InfoSp] +SummPart=merge(GroupShort,SummPart0,by="Esp") +IndexGroupe=c("Autre","Sauterelle","Chauve-souris") +SummPart$IndexSumm=match(SummPart$GroupFR,IndexGroupe) +SummPart=SummPart[with(SummPart + ,order(IndexSumm,as.numeric(Contacts_Nuit),decreasing=T)),] +colnames(SummPart)=c("Code","Groupe","Nom francais","Nom scientifique" + ,"Risque d'erreur (%)","Nb Validations" + ,"Effort de validation","Nb de Contacts par Nuit" + ,"Niveau d'Activite","TriGroupe") + +#to do: extend colors to other columns to improve readability +SummHTML=datatable(SummPart, rownames = FALSE) %>% + formatStyle(columns = c("Code","Groupe","Nom francais","Nom scientifique","Risque d'erreur (%)"),valueColumns="Risque d'erreur (%)", + background = styleInterval(c(1, 10, 50), c("white", "khaki", "orange", "orangered"))) %>% + formatStyle(columns = "Effort de validation", + background = styleEqual(c("-","FAIBLE","SUFFISANT","FORT"), c("white", "cyan", "royalblue", "darkblue"))) %>% + formatStyle(columns = c("Nb de Contacts par Nuit","Niveau d'Activite"),valueColumns="Niveau d'Activite", + background = styleEqual(c("FAIBLE","MODEREE","FORTE","TRES FORTE"), c("palegoldenrod", "greenyellow", "limegreen", "darkgreen"))) + +saveWidget(SummHTML,"output-summary.html") +write.table(SummPart,"output-summary.tabular",sep="\t",row.names=F) + +#compute number of files validated per night/hour +IdC2$Heure=sapply(IdC2$`nom du fichier`,FUN=function(x) substr(x,nchar(x)-9,nchar(x)-8)) + +ActNuit=aggregate(IdC2$`nom du fichier`,by=list(IdC2$IdExtrap,IdC2$Session),FUN=length) +ListSpref=match(ActNuit$Group.1,refPF$Espece) +Subref=refPF[ListSpref] + + +QualifActN=vector() +for (k in 1:nrow(ActNuit)) +{ + if(is.na(Subref$Q25[k])) + { + QualifActN=c(QualifActN,NA) + }else{ + cuts=cbind(-Inf,as.numeric(Subref$Q25[k]),as.numeric(Subref$Q75[k]) + ,as.numeric(Subref$Q98[k]),Inf) + + QualifActN=c(QualifActN,findInterval(ActNuit$x[k],cuts,left.open=T)) + } +} +ActNuit$QualifActN=QualifActN + +ActNuitT=dcast(data=ActNuit,formula=Group.1~Group.2 + ,value.var="x") +ActNuitT[is.na(ActNuitT)]=0 +RefNuitT=dcast(data=ActNuit,formula=Group.1~Group.2 + ,value.var="QualifActN") +ARNuit=merge(ActNuitT,RefNuitT,by="Group.1") + +SummPartshort=cbind(SummPart[,c(1:5)],TriGroupe=SummPart[,TriGroupe]) +SummPartN=merge(SummPartshort,ARNuit,by.x="Code",by.y="Group.1") +SummPartN=SummPartN[order(TriGroupe,decreasing=T),] + +test=grepl(".x",colnames(SummPartN)) +colnames(SummPartN)=mapply(FUN=function(x,y) if(y){substr(x,1,2)}else{x} + ,colnames(SummPartN),test) +ListNuit=subset(colnames(SummPartN),test) +ListRef=subset(colnames(SummPartN),grepl(".y",colnames(SummPartN))) +testHide=match(ListRef,colnames(SummPartN))-1 +#to do: extend colors to other columns to improve readability +SummHTMLN=datatable(SummPartN, rownames = FALSE,options = list( + columnDefs = list(list(targets = testHide,visible = FALSE)))) %>% + formatStyle(columns = c("Code","Groupe","Nom francais","Nom scientifique","Risque d'erreur (%)"),valueColumns="Risque d'erreur (%)", + background = styleInterval(c(1, 10, 50), c("white", "khaki", "orange", "orangered"))) %>% + formatStyle(columns = ListNuit,valueColumns=ListRef, + background = styleEqual(c(1,2,3,4), c("palegoldenrod", "greenyellow", "limegreen", "darkgreen"))) + +saveWidget(SummHTMLN,"output-nightly.html") +write.table(SummPartN,"output-nightly.tabular",sep="\t",row.names=F) + + +#summary by hour +ActMoyH=dcast(data=IdC2,formula=IdExtrap~Heure + ,fun.aggregate=length) +ActMoyHA=aggregate(IdC2$`nom du fichier` + ,by=list(IdC2$IdExtrap,IdC2$Heure) + ,FUN=length) + +test=(as.numeric(colnames(ActMoyH))>12) +ColDebut=subset(colnames(ActMoyH),test) +ColFin=subset(colnames(ActMoyH),test==F) +ListH=c(ColDebut,ColFin) +neworder=c("IdExtrap",ColDebut,ColFin) +ActMoyH=ActMoyH[,..neworder] + +SummPartH=merge(SummPartshort,ActMoyH,by.x="Code",by.y="IdExtrap") +SummPartH=SummPartH[order(TriGroupe,decreasing=T),] + + +brks <- quantile(ActMoyHA$x, probs = seq(.05, .95, .05), na.rm = TRUE)-1 +clrs <- round(seq(255, 40, length.out = length(brks) + 1), 0) %>% +{paste0("rgb(255,", ., ",", ., ")")} + + +SummHTMLH=datatable(SummPartH, rownames = FALSE) %>% + formatStyle(columns = c("Code","Groupe","Nom francais","Nom scientifique","Risque d'erreur (%)"),valueColumns="Risque d'erreur (%)", + background = styleInterval(c(1, 10, 50), c("white", "khaki", "orange", "orangered"))) %>% + formatStyle(columns=ListH, backgroundColor = styleInterval(brks, clrs)) + +saveWidget(SummHTMLH,"output-hourly.html") +write.table(SummPartH,"output-hourly.tabular",sep="\t",row.names=F) + + +#saveWidget(SummHTML,paste0(substr(args[1],1,nchar(args[1])-9),"-summary.html")) +#write.table(SummPart,paste0(substr(args[1],1,nchar(args[1])-9),"-summary.csv"),sep="\t",row.names=F) +#saveWidget(SummHTMLN,paste0(substr(args[1],1,nchar(args[1])-9),"-nightly.html")) +#write.table(SummPartN,paste0(substr(args[1],1,nchar(args[1])-9),"-nightly.csv"),sep="\t",row.names=F) +#saveWidget(SummHTMLH,paste0(substr(args[1],1,nchar(args[1])-9),"-hourly.html")) +#write.table(SummPartH,paste0(substr(args[1],1,nchar(args[1])-9),"-hourly.csv"),sep="\t",row.names=F) + + +} + + + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BilanEnrichiPFen.xml Mon Aug 06 09:13:29 2018 -0400 @@ -0,0 +1,86 @@ +<tool id="BilanEnrichiPF" name="Advanced restitution: summary" version="0.1"> + <description>from Animal Detection on Acoustic Recordings</description> + <requirements> + <requirement type="package" version="1.4.3">r-reshape2</requirement> + <requirement type="package" version="1.10.4">r-data.table</requirement> + <requirement type="package" version="0.2">r-dt</requirement> + <requirement type="package" version="0.9">r-htmlwidgets</requirement> + <requirement type="package" version="2.1.1">pandoc</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + Rscript + '$__tool_directory__/BilanEnrichiPF.R' '$IdC2' '$__tool_directory__/refPF.csv' '$__tool_directory__/SpeciesList.csv' + + && + tail -n +2 output-summary.html > tmp && mv tmp output-summary.html && + tail -n +2 output-nightly.html > tmp && mv tmp output-nightly.html && + tail -n +2 output-hourly.html > tmp && mv tmp output-hourly.html +]]> + </command> + <inputs> + <param name="IdC2" type="data" format="tabular" label="IdValid output"/> + </inputs> + <outputs> + <data name="output_summary_tabular" format="tabular" from_work_dir="output-summary.tabular" label="${tool.name} on ${on_string} Summary"/> + <data name="output_summary_html" format="html" from_work_dir="output-summary.html" label="${tool.name} on ${on_string} Summary"/> + + <data name="output_nightly_tabular" format="tabular" from_work_dir="output-nightly.tabular" label="${tool.name} on ${on_string} Nightly"/> + <data name="output_nightly_html" format="html" from_work_dir="output-nightly.html" label="${tool.name} on ${on_string} Nightly"/> + + <data name="output_hourly_tabular" format="tabular" from_work_dir="output-hourly.tabular" label="${tool.name} on ${on_string} Hourly"/> + <data name="output_hourly_html" format="html" from_work_dir="output-hourly.html" label="${tool.name} on ${on_string} Hourly"/> + </outputs> + + <tests> + <test> + <param name="IdC2" value="BilanEnrichiPF_Test1.tabular"/> + <output name="output_tab" file="BilanEnrichiPF_Test1_out_tab.tabular" ftype="tabular"/> + </test> + </tests> + + <help><![CDATA[ + +.. class:: infomark + +========================== +Advanced restitution +========================== + +**What it does** + +The tool treats observations made with the "Point fixe" protocol: https://www.vigienature-ecole.fr/node/954> + +**Arguments** + +- Input is an observation/participation file corrected by the tools IdCorrect_2ndLayer and IdValid. +- Outputs are Summary/Nightly/Hourly raw tabulars, and html visualisations. + + ]]></help> + + <citations> + <citation type="bibtex"> + @article{kerbiriou2015vigie, + title={Vigie-Chiro: 9 ans de suivi des tendances des esp{\`e}ces communes}, + author={Kerbiriou, C and Julien, JF and Bas, Y and Marmet, J and Le Viol, I and Lorrilliere, R and Azam, C and Gasc, A and Lois, G}, + journal={Symbioses, nouvelle s{\'e}rie}, + number={34}, + year={2015} + } + </citation> + <citation type="bibtex"> + @inproceedings{bas2013automatic, + title={Automatic echolocation calls identification in Europe vs. Neotropics: more species does not mean more difficult}, + author={Bas, Yves and Escallon, Antoine and Ferre, Matthieu and Haquart, Alexandre and Rufray, Vincent and Disca, Thierry and Julien, Jean-Fran{\c{c}}ois} + } + </citation> + <citation type="bibtex"> + @inproceedings{kerbiriou2010long, + title={Long term trends monitoring of bats, from biodiversity indicator production to species specialization assessment}, + author={Kerbiriou, C and Bas, Y and Dufr{\^e}ne, L and Robert, A and Julien, JF}, + booktitle={24th Annual Meeting of the Society for Conservation Biology, Edmonton, Canada}, + year={2010} + } + </citation> + <citation type="doi">10.5334/jors.154</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BilanEnrichiRP.R Mon Aug 06 09:13:29 2018 -0400 @@ -0,0 +1,238 @@ +library(data.table) +library(DT) +library(htmlwidgets) + +args <- commandArgs(trailingOnly = TRUE) +#print(args) +EchelleErreur=c("","POSSIBLE","PROBABLE","SUR") +EchelleNumErreur=c(99,50,10,1) + +#for test +#inputest=list.files("C:/Users/Yves Bas/Documents/GitHub/65MO_Galaxy-E/raw_scripts/Vigie-Chiro/output_IdValid_input_BilanEnrichi/",pattern="IdC2.csv",full.names=T) +#for (i in 1:length(inputest)) +#{ +# args=c(inputest[i],"refRPSeuil50.csv","SpeciesList.csv") + +IdC2=fread(args[1]) +refRP=fread(args[2]) +GroupList=fread(args[3]) + + +if(substr(IdC2$`nom du fichier`[1],2,2)!="i") +{ + print("Protocole non conforme, ce script doit etre lance pour un protocole Routier ou Pedestre") +}else{ + +Routier=grepl("-",substr(IdC2$`nom du fichier`[1],4,7)) +#compute error risk by species (minimum error among files) +#to be replaced by glm outputs if I'll have time +RisqueErreurT=aggregate(IdC2$IdProb,by=list(IdC2$IdExtrap),FUN=function(x) ceiling((1-max(x-0.0001))*100)) +barplot(RisqueErreurT$x,names.arg=RisqueErreurT$Group.1,las=2) +#compute error risk accoring to observer/validator (a little dirty because it relies on alphabetical order of confidence classes: POSSIBLE < PROBABLE < SUR) +RisqueErreurOV0=match(IdC2$ConfV,EchelleErreur) +RisqueErreurOV=aggregate(RisqueErreurOV0,by=list(IdC2$IdExtrap) + ,FUN=max) +RisqueErreurOV2=EchelleNumErreur[RisqueErreurOV$x] +#compute minimum error risk between man and machine +RisqueErreur=pmin(RisqueErreurT$x,RisqueErreurOV2) + +#compute number of files validated per species +FichValid=aggregate(IdC2$IdV,by=list(IdC2$IdExtrap,IdC2$'nom du fichier') + ,FUN=function(x) sum(x!="")) +NbValid2=aggregate(FichValid$x,by=list(FichValid$Group.1),FUN=function(x) sum(x>0)) + +DiffC50=vector() # to store the median of confidence difference between unvalidated records and validated ones +DiffT50=vector() # to store the median of time difference between unvalidated records and validated ones +for (j in 1:nlevels(as.factor(IdC2$IdExtrap))) +{ + IdSp=subset(IdC2 + ,IdC2$IdExtrap==levels(as.factor(IdC2$IdExtrap))[j]) + IdSp$IdProb[is.na(IdSp$IdProb)]=0 + IdSp=IdSp[order(IdSp$IdProb),] + IdSpV=subset(IdSp,IdSp$IdV!="") + if(nrow(IdSpV)>0) + { + cuts <- c(-Inf, IdSpV$IdProb[-1]-diff(IdSpV$IdProb)/2, Inf) + CorrC=findInterval(IdSp$IdProb, cuts) + CorrC2=IdSpV$IdProb[CorrC] + DiffC=abs(IdSp$IdProb-CorrC2) + DiffC50=c(DiffC50,median(DiffC)) + + IdSp=IdSp[order(IdSp$TimeNum),] + IdSpV=subset(IdSp,IdSp$IdV!="") + cuts <- c(-Inf, IdSpV$TimeNum[-1]-diff(IdSpV$TimeNum)/2, Inf) + CorrT=findInterval(IdSp$TimeNum, cuts) + CorrT2=IdSpV$TimeNum[CorrT] + DiffT=abs(IdSp$TimeNum-CorrT2) + DiffT50=c(DiffT50,median(DiffT)) + }else{ + DiffC50=c(DiffC50,Inf) + DiffT50=c(DiffT50,Inf) + } +} +#compute an index of validation effort per species +EffortV=1/DiffC50/DiffT50 +EffortClass=(EffortV>0.0005)+(EffortV>0.005)+RisqueErreurOV$x +#cbind(RisqueErreurOV,EffortV,DiffC50,DiffT50) +barplot(EffortClass-1,names.arg=NbValid2$Group.1,las=2) +ClassEffortV=c("-","FAIBLE","SUFFISANT","SUFFISANT","FORT","FORT") +EffortClassMot=ClassEffortV[EffortClass] + + +#compare activity / reference frame +FileInfo=as.data.table(tstrsplit(IdC2$`nom du fichier`,"-")) +IdC2$Tron=FileInfo$V4 + +MicTempsInfo=as.data.table(tstrsplit(as.data.frame(FileInfo)[,(ncol(FileInfo))],"_")) +MicDroit=(as.data.frame(MicTempsInfo)[,(ncol(MicTempsInfo)-2)]=="1") +IdC2$MicDroit=MicDroit + +testTempsFin=aggregate(IdC2$temps_fin,by=list(MicDroit),FUN=max) +testTempsFin$Direct=(testTempsFin$x>0.5) +testTF2=sum((testTempsFin$x>0.5)) +if(testTF2>1){stop("Probleme stereo : les 2 canaux semblent etre en enregistrement direct")} +IdC2M=merge(IdC2,testTempsFin,by.x="MicDroit",by.y="Group.1") + +ActMoy=aggregate(IdC2$`nom du fichier` + ,by=list(IdC2M$IdExtrap,IdC2M$Direct),FUN=length) +ListSpref=match(levels(as.factor(ActMoy$Group.1)),refRP$Espece) +Subref=refRP[ListSpref] +if(Routier) +{ + Subref=Subref[,c(1:17)] +}else{ + Subref=Subref[,c(1,18:33)] +} +QualifActE=vector() +QualifActD=vector() + +for (k in 1:nlevels(as.factor(ActMoy$Group.1))) +{ + Actsub=subset(ActMoy,ActMoy$Group.1==levels(as.factor(ActMoy$Group.1))[k]) + if(is.na(Subref[k,2])) + { + QualifActE=c(QualifActE,NA) + QualifActD=c(QualifActD,NA) + }else{ + ActE=subset(Actsub,Actsub$Group.2==F) + if(nrow(ActE)==0) + { + QualifActE=c(QualifActE,NA) + + }else{ + cuts=cbind(-Inf,as.numeric(Subref[k,6]),as.numeric(Subref[k,7]) + ,as.numeric(Subref[k,8]),Inf) + QualifActE=c(QualifActE,findInterval(ActE$x,cuts,left.open=T)) + } + ActD=subset(Actsub,Actsub$Group.2==T) + if(nrow(ActD)==0) + { + QualifActD=c(QualifActD,NA) + + }else{ + cuts=cbind(-Inf,as.numeric(Subref[k,14]),as.numeric(Subref[k,15]) + ,as.numeric(Subref[k,16]),Inf) + QualifActD=c(QualifActD,findInterval(ActD$x,cuts,left.open=T)) + } + + } +} +ClassAct=c("FAIBLE","MODEREE","FORTE","TRES FORTE") +QualifActMotE=ClassAct[QualifActE] +QualifActMotD=ClassAct[QualifActD] + +#compute activity by nights (to be completed) +#ActNuit=aggregate(IdC2M$`nom du fichier`,by=list(IdC2M$DateNuit,IdC2M$IdExtrap),FUN=length) +ActED=dcast(data=ActMoy,formula=Group.1~Group.2,value=x) +ActED[is.na(ActED)]=0 +#organize the csv summary +SummPart0=cbind(Esp=levels(as.factor(IdC2M$IdExtrap)) + ,RisqueErreur,NbValid=NbValid2$x,EffortValid=EffortClassMot) + +test=match("FALSE",colnames(ActED)) +if(is.na(test)==F) +{ + SummPart0=cbind(SummPart0,Contacts_Expansion=ActED$'FALSE' + ,Niveau_Activite_Expansion=QualifActMotE) +}else{ + SummPart0=cbind(SummPart0,Contacts_Expansion="" + ,Niveau_Activite_Expansion="") +} +test=match("TRUE",colnames(ActED)) +if(is.na(test)==F) +{ + + SummPart0=cbind(SummPart0,Contacts_Direct=ActED$'TRUE' + ,Niveau_Activite_Direct=QualifActMotD) +}else{ + SummPart0=cbind(SummPart0,Contacts_Direct="" + ,Niveau_Activite_Direct="") +} + +InfoSp=c("GroupFR","NomFR","Scientific name","Esp") +GroupShort=GroupList[,..InfoSp] +SummPart=merge(GroupShort,SummPart0,by="Esp") +IndexGroupe=c("Autre","Sauterelle","Chauve-souris") +SummPart$IndexSumm=match(SummPart$GroupFR,IndexGroupe) +SummPart=SummPart[with(SummPart + ,order(IndexSumm,as.numeric(Contacts_Direct),as.numeric(Contacts_Expansion),decreasing=T)),] +colnames(SummPart)=c("Code","Groupe","Nom francais","Nom scientifique" + ,"Risque d'erreur (%)","Nb Validations" + ,"Effort de validation","Nb de Contacts en expansion" + ,"Niveau d'Activite en expansion" + ,"Nb de Contacts en direct" + ,"Niveau d'Activite en direct","TriGroupe") + +#to do: extend colors to other columns to improve readability +SummHTML=datatable(SummPart, rownames = FALSE) %>% + formatStyle(columns = c("Code","Groupe","Nom francais","Nom scientifique","Risque d'erreur (%)"),valueColumns="Risque d'erreur (%)", + background = styleInterval(c(1, 10, 50), c("white", "khaki", "orange", "orangered"))) %>% + formatStyle(columns = "Effort de validation", + background = styleEqual(c("-","FAIBLE","SUFFISANT","FORT"), c("white", "cyan", "royalblue", "darkblue"))) %>% + formatStyle(columns = c("Nb de Contacts en expansion","Niveau d'Activite en expansion"),valueColumns="Niveau d'Activite en expansion", + background = styleEqual(c("FAIBLE","MODEREE","FORTE","TRES FORTE"), c("palegoldenrod", "greenyellow", "limegreen", "darkgreen"))) %>% + formatStyle(columns = c("Nb de Contacts en direct","Niveau d'Activite en direct"),valueColumns="Niveau d'Activite en direct", + background = styleEqual(c("FAIBLE","MODEREE","FORTE","TRES FORTE"), c("palegoldenrod", "greenyellow", "limegreen", "darkgreen"))) + + +saveWidget(SummHTML,"output-summaryRP.html") +write.table(SummPart,"output-summaryRP.tabular",row.names=F,sep="\t") + +#summary for each point/transect + +#compute number of files validated per species +IdC2M$Canal=sapply(IdC2M$Direct,FUN=function(x) if(x){"Direct"}else{"Expansion"}) + +ActMoyTA=aggregate(IdC2M$`nom du fichier`,by=list(IdC2M$IdExtrap,IdC2M$Canal,IdC2M$Session),FUN=length) +ActMoyT=dcast(data=IdC2M,formula=IdExtrap+Canal~Session + ,fun.aggregate=length) +SummPartshort=cbind(SummPart[,c(1:5)],TriGroupe=SummPart[,TriGroupe]) +SummPartTron=merge(SummPartshort,ActMoyT,by.x="Code",by.y="IdExtrap") +SummPartTron=SummPartTron[order(TriGroupe,decreasing=T),] + +ListSession=levels(as.factor(IdC2M$Session)) +brks <- quantile(ActMoyTA$x, probs = seq(.05, .95, .05), na.rm = TRUE)-1 +clrs <- round(seq(255, 40, length.out = length(brks) + 1), 0) %>% +{paste0("rgb(255,", ., ",", ., ")")} + + +#to do: extend colors to other columns to improve readability +SummHTMLT=datatable(SummPartTron, rownames = FALSE) %>% + formatStyle(columns = c("Code","Groupe","Nom francais","Nom scientifique","Risque d'erreur (%)"),valueColumns="Risque d'erreur (%)", + background = styleInterval(c(1, 10, 50), c("white", "khaki", "orange", "orangered"))) %>% + formatStyle(columns=ListSession, backgroundColor = styleInterval(brks, clrs)) + +saveWidget(SummHTMLT,"output-detailRP.html") +write.table(SummPartTron,"output-detailRP.tabular",row.names=F,sep="\t") + +#saveWidget(SummHTML,paste0(substr(args[1],1,nchar(args[1])-9),"-summary.html")) +#write.table(SummPart,paste0(substr(args[1],1,nchar(args[1])-9),"-summary.csv"),row.names=F,sep="\t") +#saveWidget(SummHTMLT,paste0(substr(args[1],1,nchar(args[1])-9),"-detail.html")) +#write.table(SummPartTron,paste0(substr(args[1],1,nchar(args[1])-9),"-detail.csv"),row.names=F,sep="\t") + + + +} + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BilanEnrichiRPen.xml Mon Aug 06 09:13:29 2018 -0400 @@ -0,0 +1,74 @@ +<tool id="BilanEnrichiRP" name="Advanced restitution: raw approach" version="0.1"> + <description>from Animal Detection on Acoustic Recordings</description> + <requirements> + <requirement type="package" version="1.4.3">r-reshape2</requirement> + <requirement type="package" version="1.10.4">r-data.table</requirement> + <requirement type="package" version="0.2">r-dt</requirement> + <requirement type="package" version="0.9">r-htmlwidgets</requirement> + <requirement type="package" version="2.1.1">pandoc</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + Rscript + '$__tool_directory__/BilanEnrichiRP.R' '$IdC2' '$__tool_directory__/refRPSeuil50.csv' '$__tool_directory__/SpeciesList.csv' + && + tail -n +2 output-summaryRP.html > tmp && mv tmp output-summaryRP.html && + tail -n +2 output-detailRP.html > tmp && mv tmp output-detailRP.html +]]> + </command> + <inputs> + <param name="IdC2" type="data" format="tabular" label="IdValid output"/> + </inputs> + <outputs> + <data name="output_summary_tabular" format="tabular" from_work_dir="output-summaryRP.tabular" label="${tool.name} on ${on_string} Summary"/> + <data name="output_summary_html" format="html" from_work_dir="output-summaryRP.html" label="${tool.name} on ${on_string} Summary"/> + <data name="output_detail_tabular" format="tabular" from_work_dir="output-detailRP.tabular" label="${tool.name} on ${on_string} Detail"/> + <data name="output_detail_html" format="html" from_work_dir="output-detailRP.html" label="${tool.name} on ${on_string} Detail"/> + </outputs> + + <tests> + <test> + <param name="IdC2" value="BilanEnrichiPF_Test1.tabular"/> + <output name="output_tab" file="BilanEnrichiPF_Test1_out_tab.tabular" ftype="tabular"/> + </test> + </tests> + + <help><![CDATA[ +**What it does** + +The tool analyses the observations made with the "Routier" or "Pedestre" protocols. + +**Arguments** + +- Input is an observation/participation file corrected by the tools IdCorrect_2ndLayer and IdValid. +- Outputs are Summary and details raw tabulars, and html visualisations. + + + ]]></help> + + <citations> + <citation type="bibtex"> + @article{kerbiriou2015vigie, + title={Vigie-Chiro: 9 ans de suivi des tendances des esp{\`e}ces communes}, + author={Kerbiriou, C and Julien, JF and Bas, Y and Marmet, J and Le Viol, I and Lorrilliere, R and Azam, C and Gasc, A and Lois, G}, + journal={Symbioses, nouvelle s{\'e}rie}, + number={34}, + year={2015} + } + </citation> + <citation type="bibtex"> + @inproceedings{bas2013automatic, + title={Automatic echolocation calls identification in Europe vs. Neotropics: more species does not mean more difficult}, + author={Bas, Yves and Escallon, Antoine and Ferre, Matthieu and Haquart, Alexandre and Rufray, Vincent and Disca, Thierry and Julien, Jean-Fran{\c{c}}ois} + } + </citation> + <citation type="bibtex"> + @inproceedings{kerbiriou2010long, + title={Long term trends monitoring of bats, from biodiversity indicator production to species specialization assessment}, + author={Kerbiriou, C and Bas, Y and Dufr{\^e}ne, L and Robert, A and Julien, JF}, + booktitle={24th Annual Meeting of the Society for Conservation Biology, Edmonton, Canada}, + year={2010} + } + </citation> + <citation type="doi">10.5334/jors.154</citation> +</citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GroupList_HF.csv Mon Aug 06 09:13:29 2018 -0400 @@ -0,0 +1,112 @@ +Nesp;France;Turquie;Espagne;Norfolk;Scientific name;Group;Seuil_grossier;NomFR;GroupFR +amph;x;x;x;x;Amphibia sp.;frog;0;Amphibien sp.;Autre +Antius;x;;x;;Antaxius spinibrachius;bush-cricket;0;Antaxie voyageuse;Sauterelle +Antped;x;;;;Antaxius pedestris;bush-cricket;0.6;Antaxie marbree;Sauterelle +Antsor;x;;;;Antaxius sorrezensis;bush-cricket;0;Antaxie cevenole;Sauterelle +Aposp;x;x;x;;Apodemus sp.;other mammal;0;Mulot sp.;Autre +Barbar;x;x;x;x;Barbastella barbastellus;bat;0.45;Barbastelle d'Europe;Chauve-souris +Barfis;x;;;;Barbitistes fischeri;bush-cricket;0.25;Barbitiste languedocien;Sauterelle +Barsan;x;;x;;Barbitistes cf. sanzii;bush-cricket;0;Barbitiste cryptique;Sauterelle +Barser;x;;x;;Barbitistes serricauda;bush-cricket;0;Barbitiste des bois;Sauterelle +Bicbic;x;;x;;Bicolorana bicolor;bush-cricket;0.5;Decticelle bicolore;Sauterelle +chirp;x;;;;chirp;noise;0;chirp;Autre +Cicorn;x;x;x;;Cicada orni;cicada;0;Cigale grise;Autre +Condor;x;x;x;x;Conocephalus dorsalis;bush-cricket;0.7;Conocephale des marais;Sauterelle +Confus;x;;x;x;Conocephalus fuscus;bush-cricket;0.7;Conocephale bigarre;Sauterelle +criq;x;x;x;x;Acrididae sp.;grasshopper;0;Criquet sp.;Autre +Cympud;x;;x;;Cymbalophora pudica;moth;0;Ecaille pudique;Autre +Cyrscu;x;;x;;Cyrtaspis scutatus;bush-cricket;0;Meconeme a bouclier;Sauterelle +Decalb;x;x;x;;Decticus albifrons;bush-cricket;0;Dectique a front blanc;Sauterelle +Epheph;x;;x;;Ephippiger ephippiger;bush-cricket;0.7;Ephippigere des vignes;Sauterelle +Eptana;;x;;;Eptesicus anatolicus;bat;0;Serotine d'Anatolie;Chauve-souris +Eptisa;;;x;;Eptesicus isabellinus;bat;0;Serotine isabelle;Chauve-souris +Eptser;x;x;x;x;Eptesicus serotinus;bat;0.35;Serotine commune;Chauve-souris +Eumbor;x;x;x;;Eumodycogryllus bordigalensis;ground-cricket;0;Grillon bordelais;Autre +Eupcha;x;x;;;Eupholidoptera chabrieri;bush-cricket;0;Decticelle splendide;Sauterelle +Hypsav;x;x;x;;Hypsugo savii;bat;0.63;Vespere de Savi;Chauve-souris +Inssp1;x;;x;x;Insect sp.1;insect;0;Insecte sp. type 1;Autre +Inssp2;x;;x;x;Insect sp.2;insect;0;Insecte sp. type 2;Autre +Inssp5;x;;x;x;Insect sp.5;insect;0;Insecte sp. type 5;Autre +Inssp6;x;;x;x;Insect sp.6;insect;0;Insecte sp. type 6;Autre +Inssp7;x;;x;x;Insect sp.7;insect;0;Insecte sp. type 7;Autre +InsTu1;;x;;;Insect sp. from Turkey 1;insect;0;Insecte sp. Tu1;Autre +Isopyr;x;x;x;;Isophya pyrenea;bush-cricket;0.6;Barbatiste pyreneen;Sauterelle +Lamsp.;x;x;x;x;Lampyris sp.;beetle;0;Lampyre sp.;Autre +Lepalb;;x;;;Leptophyes albovittata;bush-cricket;0;Sauterelle rayee;Sauterelle +Lepbos;x;;;;Leptophyes boscii;bush-cricket;0;Sauterelle sarmate;Sauterelle +Leppun;x;;x;x;Leptophyes punctatissima;bush-cricket;0.7;Sauterelle ponctuee;Sauterelle +Llusta;;;x;;Lluciapomaresius stalii;bush-cricket;0;Ephippigere de Stal;Sauterelle +mamm;x;x;x;x;Mammalia sp.;other mammal;0;Mammifere sp.;Autre +Metbra;x;;;x;Metrioptera brachyptera;bush-cricket;0;Decticelle des bruyeres;Sauterelle +Micagr;x;x;x;x;Microtus agrestis;other mammal;0;Campagnol agreste;Autre +Minsch;x;x;x;;Miniopterus schreibersii;bat;0.57;Minioptere;Chauve-souris +Mussp;x;x;x;x;Crocidura russula;other mammal;0;Musaraigne sp.;Autre +Myoalc;x;x;x;x;Myotis alcathoe;bat;0.35;Murin d'Alcathoe;Chauve-souris +Myobec;x;x;x;x;Myotis bechsteinii;bat;0;Murin de Bechstein;Chauve-souris +Myobra;x;x;;x;Myotis brandtii;bat;0;Murin de Brandt;Chauve-souris +Myocap;x;x;x;;Myotis capaccinii;bat;0.69;Murin de Capaccini;Chauve-souris +Myodas;x;x;;;Myotis dasycneme;bat;0;Murin des marais;Chauve-souris +Myodau;x;x;x;x;Myotis daubentonii;bat;0.27;Murin de Daubenton;Chauve-souris +Myoema;x;x;x;x;Myotis emarginatus;bat;0.42;Murin a oreilles echancrees;Chauve-souris +MyoGT;x;x;x;;Myotis cf. myotis;bat;0.35;Murin de grande taille;Chauve-souris +Myomys;x;x;x;x;Myotis mystacinus;bat;0.55;Murin a moustaches;Chauve-souris +Myonat;x;x;;x;Myotis cf. nattereri;bat;0.46;Murin groupe Natterer;Chauve-souris +noise;x;x;x;x;noise;noise;0;bruit;Autre +Nyclas;x;x;x;;Nyctalus lasiopterus;bat;0.5;Grande Noctule;Chauve-souris +Nyclei;x;x;x;x;Nyctalus leisleri;bat;0.42;Noctule de Leisler;Chauve-souris +Nycnoc;x;x;x;x;Nyctalus noctula;bat;0.5;Noctule commune;Chauve-souris +Odomac;;;x;;Odontura macphersoni;bush-cricket;0;Sauterelle de MacPherson;Sauterelle +Phafal;x;x;x;;Phaneroptera falcata;bush-cricket;0;Phaneroptere commun;Sauterelle +Phanan;x;x;x;;Phaneroptera nana;bush-cricket;0.55;Phaneroptere meridional;Sauterelle +Phofem;x;x;;;Pholidoptera femorata;bush-cricket;0;Decticelle des friches;Sauterelle +Phogri;x;x;x;x;Pholidoptera griseoaptera;bush-cricket;0.8;Decticelle cendree;Sauterelle +piaf;x;x;x;x;Aves sp.;bird;0;Oiseau sp.;Autre +Pipkuh;x;x;x;x;Pipistrellus kuhlii;bat;0.43;Pipistrelle de Kuhl;Chauve-souris +Pipnat;x;x;x;x;Pipistrellus nathusii;bat;0.68;Pipistrelle de Nathusius;Chauve-souris +Pippip;x;x;x;x;Pipistrellus pipistrellus;bat;0.24;Pipistrelle commune;Chauve-souris +Pippyg;x;x;x;x;Pipistrellus pygmaeus;bat;0.68;Pipistrelle soprane;Chauve-souris +Plaaff;x;;x;;Platycleis affinis;bush-cricket;0;Decticelle cotiere;Sauterelle +Plaalb;x;;x;x;Platycleis albopunctata;bush-cricket;0;Decticelle chagrinee;Sauterelle +Plafal;x;;x;;Platycleis falx;bush-cricket;0;Decticelle a serpe;Sauterelle +Plaibe;;;x;;Platycleis iberica;bush-cricket;0;Decticelle iberique;Sauterelle +Plaint;x;;x;;Platycleis intermedia;bush-cricket;0;Decticelle intermediaire;Sauterelle +Plasab;x;;x;;Platycleis sabulosa;bush-cricket;0;Decticelle des sables;Sauterelle +Pleaur;x;;x;x;Plecotus auritus;bat;0.3;Oreillard roux;Chauve-souris +Pleaus;x;;x;x;Plecotus austriacus;bat;0.52;Oreillard gris;Chauve-souris +Plekol;;x;;;Plecotus kolombatovici;bat;0;Oreillard des Balkans;Chauve-souris +Plemac;x;x;x;;Plecotus macrobullaris;bat;0.5;Oreillard montagnard;Chauve-souris +Pteger;x;x;;;Pterolepis germanica;bush-cricket;0;Decticelle orientale;Sauterelle +Ptegra;;x;x;;Pterolepis grallata;bush-cricket;0;Decticelle a pattes fines;Sauterelle +Ptepon;x;x;x;;Pterolepis poneli;bush-cricket;0;Decticelle varoise;Sauterelle +Pycjug;;;x;;Pycnogaster jugicola;bush-cricket;0;Ephippigere droite;Sauterelle +Ratnor;x;x;x;x;Rattus norvegicus;other mammal;0;Surmulot;Autre +Rhibla;x;x;;;Rhinolophus blasii;bat;0;Rhinolophe de Blasius;Chauve-souris +Rhieur;x;x;x;;Rhinolophus euryale;bat;0.2;Rhinolophe euryale;Chauve-souris +Rhifer;x;x;x;x;Rhinolophus ferrumequinum;bat;0.3;Grand Rhinolophe;Chauve-souris +Rhihip;x;x;x;x;Rhinolophus hipposideros;bat;0.53;Petit Rhinolophe;Chauve-souris +Rhimeh;;x;x;;Rhinolophus mehelyi;bat;0;Rinolophe de Mehely;Chauve-souris +Roeroe;x;x;x;x;Roeseliana roeselii;bush-cricket;0;Decticelle bariolee;Sauterelle +Rusnit;x;x;x;x;Ruspolia nitidula;bush-cricket;0;Conocephale gracieux;Sauterelle +SauTu4;;x;;;Tettigoniidae sp. from Turkey 4;bush-cricket;0;Sauterelle sp. Tu4;Sauterelle +SauTu5;;x;;;Tettigoniidae sp. from Turkey 5;bush-cricket;0;Sauterelle sp. Tu5;Sauterelle +SauTu6;;x;;;Tettigoniidae sp. from Turkey 6;bush-cricket;0;Sauterelle sp. Tu6;Sauterelle +SauTu7;;x;;;Tettigoniidae sp. from Turkey 7;bush-cricket;0;Sauterelle sp. Tu7;Sauterelle +SauTurquiesp1;;x;;;Tettigoniidae sp. from Turkey 1;bush-cricket;0;Sauterelle sp. Tu1;Sauterelle +SauTurquiesp2;;x;;;Tettigoniidae sp. from Turkey 2;bush-cricket;0;Sauterelle sp. Tu2;Sauterelle +SauTurquiesp3;;x;;;Tettigoniidae sp. from Turkey 3;bush-cricket;0;Sauterelle sp. Tu3;Sauterelle +Sepsep;x;;x;;Sepiana sepium;bush-cricket;0;Decticelle echassiere;Sauterelle +Tadten;x;x;x;;Tadarida teniotis;bat;0.4;Molosse;Chauve-souris +Tesori;;;;;Tessellana orina;bush-cricket;0;Decticelle orina;Sauterelle +Testes;x;x;x;;Tessellana tessellata;bush-cricket;0;Decticelle carroyee;Sauterelle +Tetarg;x;;x;;Tettigetta argentata;cicada;0;Cigale argentee;Autre +Tetcan;x;x;x;;Tettigonia cantans;bush-cricket;0;Sauterelle cymbaliere;Sauterelle +Tethis;;;x;;Tettigonia hispanica;bush-cricket;0;Sauterelle hispanique;Sauterelle +Tetpyg;x;;x;;Tettigetta pygmea;cicada;0;Cigale pygmee;Autre +Tetvir;x;x;x;x;Tettigonia viridissima;bush-cricket;0;Sauterelle verte;Sauterelle +Thycor;x;;x;;Thyreonotus corsicus;bush-cricket;0;Decticelle marocaine;Sauterelle +Tyllil;x;x;x;;Tylopsis lilifolia;bush-cricket;0;Phaneroptere liliace;Sauterelle +Urorug;x;;x;;Uromenus rugosicollis;bush-cricket;0;Ephippigere carenee;Sauterelle +Vesmur;x;x;x;;Vespertilio murinus;bat;0.5;Serotine bicolore;Chauve-souris +Yerbey;x;;;;Yersinella beybienkoi;bush-cricket;0;Decticelle italienne;Sauterelle +Yerray;x;;x;;Yersinella raymondii;bush-cricket;0;Decticelle frele;Sauterelle +Zeuabb;x;;x;;Zeuneriana abbreviata;bush-cricket;0;Decticelle aquitaine;Sauterelle
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/IdCorrect_2ndLayer.R Mon Aug 06 09:13:29 2018 -0400 @@ -0,0 +1,181 @@ +library(data.table) +library(randomForest) +args <- commandArgs(trailingOnly = TRUE) + +set.seed(1) #To test reproductibility + + +#for test +#inputest=list.files("C:/Users/Yves Bas/Documents/GitHub/65MO_Galaxy-E/raw_scripts/Vigie-Chiro/input_examples",full.names=T,pattern="participation-") +#for (i in 1:length(inputest)) +#{ +# args=c(inputest[i],"ClassifEspC2b_180222.learner") +#args[3]=basename(args[1]) + +filename=args[3] +if (exists("ClassifEspC2b")==F){load(args[2])} + +DataPar=fread(args[1]) #id to be corrected +DataPar$participation=substr(filename,nchar(filename)-40,nchar(filename)-17) +test1=duplicated(cbind(DataPar$'nom du fichier',DataPar$tadarida_taxon)) +test2=(DataPar$tadarida_taxon=="empty") +DataPar=subset(DataPar,(!test1)|(test2)) +DataPar$tadarida_probabilite[DataPar$tadarida_probabilite==""]="0" +DataPar$tadarida_probabilite=as.numeric(DataPar$tadarida_probabilite) + + +#tableau comptabilisant le nombre de contacts par espèces +nbcT=as.matrix(table(DataPar$participation,DataPar$tadarida_taxon)) + +DataPar$tadarida_probabilite=as.numeric(DataPar$tadarida_probabilite) + +#generating input variables for second layer classification + +Q25=vector() +Q50=vector() +Q75=vector() +Q90=vector() +Q95=vector() +Q98=vector() +Q100=vector() +compt=0 +PropSp=nbcT[0,] +VoteO=DataPar[0,] +for (j in 1:nlevels(as.factor(DataPar$tadarida_taxon))) + { + Datasub2=subset(DataPar,DataPar$tadarida_taxon==levels(as.factor(DataPar$tadarida_taxon))[j]) + + Q25=c(Q25,rep(quantile(Datasub2$tadarida_probabilite,0.25),nrow(Datasub2))) + Q50=c(Q50,rep(quantile(Datasub2$tadarida_probabilite,0.50),nrow(Datasub2))) + Q75=c(Q75,rep(quantile(Datasub2$tadarida_probabilite,0.75),nrow(Datasub2))) + Q90=c(Q90,rep(quantile(Datasub2$tadarida_probabilite,0.90),nrow(Datasub2))) + Q95=c(Q95,rep(quantile(Datasub2$tadarida_probabilite,0.95),nrow(Datasub2))) + Q98=c(Q98,rep(quantile(Datasub2$tadarida_probabilite,0.98),nrow(Datasub2))) + Q100=c(Q100,rep(max(Datasub2$tadarida_probabilite),nrow(Datasub2))) + Ncont1=nrow(Datasub2) + VoteO=rbind(VoteO,Datasub2) + PropSp0=nbcT/Ncont1 + PropSp=rbind(PropSp,PropSp0[rep(seq_len(nrow(PropSp0)),nrow(Datasub2)),]) + compt=compt+nrow(Datasub2) + #print(paste(compt,levels(as.factor(DataPar$tadarida_taxon))[j])) + } + +VoteC2=cbind(VoteO,PropSp,Q25,Q50,Q75,Q90,Q95,Q98,Q100) + + +#édition des titres de colonne pour identifier les variables de type "proportions d'abondances" +for (i in 15:(ncol(VoteC2)-7)) +{ + colnames(VoteC2)[i]=paste0(names(VoteC2)[i],"_prop") +} + +#rajouter les espèces manquantes +EspForm=subset(row.names(ClassifEspC2b$importance) + ,substr(row.names(ClassifEspC2b$importance) + ,nchar(row.names(ClassifEspC2b$importance))-4 + ,nchar(row.names(ClassifEspC2b$importance))) + =="_prop") +test=match(EspForm,colnames(VoteC2)) +EspM=subset(EspForm,is.na(test)) +Zeros=matrix(nrow=nrow(VoteC2),ncol=length(EspM)) +Zeros[is.na(Zeros)]=0 +colnames(Zeros)=EspM +VoteC2=cbind(VoteC2,Zeros) + +ListDV=levels(as.factor(DataPar$'nom du fichier')) +#calcule les probabilités max par espèce et par fichier +#(utile pour corriger les erreurs dues à la coexistence de taxons dans le même fichier +#ex: cris sociaux de Pipistrelles identifiées comme autre chose (Noctule, oreillard...)) +MaxI=tapply(DataPar$tadarida_probabilite + ,INDEX=list(c(DataPar$'nom du fichier'),c(DataPar$tadarida_taxon)) + ,FUN=max) +MaxI2=as.data.frame(cbind(row.names(MaxI),MaxI)) +for (i in 2:ncol(MaxI2)) +{ + MaxI2[,i]=as.numeric(as.character(MaxI2[,i])) +} +MaxI2[is.na(MaxI2)]=0 + +#édition des titres de colonne pour identifier les variables de type "indices max" +for (i in 2:(ncol(MaxI2))) +{ + colnames(MaxI2)[i]=paste0(names(MaxI2)[i],"_maxI") +} + + +#rajouter les espèces manquantes +EspForm=subset(row.names(ClassifEspC2b$importance) + ,substr(row.names(ClassifEspC2b$importance) + ,nchar(row.names(ClassifEspC2b$importance))-4 + ,nchar(row.names(ClassifEspC2b$importance))) + =="_maxI") +test=match(EspForm,colnames(MaxI2)) +EspM=subset(EspForm,is.na(test)) +Zeros=matrix(nrow=nrow(MaxI2),ncol=length(EspM)) +Zeros[is.na(Zeros)]=0 +colnames(Zeros)=EspM +MaxI2=cbind(MaxI2,Zeros) + + + + +#indice de confiance à l'echelle de l'observation (groupe de cris identifié comme provenant d'une seule espèce par la première couche) +if(exists("IdS3")){rm(IdS3)} +for (i in 1:nlevels(as.factor(DataPar$tadarida_taxon))) +{ + Idsub=subset(DataPar,DataPar$tadarida_taxon==levels(as.factor(DataPar$tadarida_taxon))[i]) + IdS2=cbind('nom du fichier'=Idsub$'nom du fichier',tadarida_taxon=Idsub$tadarida_taxon,prob=Idsub$tadarida_probabilite) + colnames(IdS2)[3]=paste(levels(as.factor(DataPar$tadarida_taxon))[i]) + if(exists("IdS3")){IdS3=merge(IdS3,IdS2,all=T)}else{IdS3=IdS2} + #print(i) +} + +for (i in 3:ncol(IdS3)) +{ + IdS3[,i]=as.numeric(as.character(IdS3[,i])) +} + +#édition des titres de colonne pour identifier les variables de type "indices de l'observation" +for (i in 3:(ncol(IdS3))) +{ + colnames(IdS3)[i]=paste0(names(IdS3)[i],"_ValI") +} + +IdS3[is.na(IdS3)]=0 + +#rajouter les espèces manquantes +EspForm=subset(row.names(ClassifEspC2b$importance) + ,substr(row.names(ClassifEspC2b$importance) + ,nchar(row.names(ClassifEspC2b$importance))-4 + ,nchar(row.names(ClassifEspC2b$importance))) + =="_ValI") +test=match(EspForm,colnames(IdS3)) +EspM=subset(EspForm,is.na(test)) +Zeros=matrix(nrow=nrow(IdS3),ncol=length(EspM)) +Zeros[is.na(Zeros)]=0 +colnames(Zeros)=EspM +IdS3=cbind(IdS3,Zeros) + +#on merge les prop d'espèces, les quantiles et les indices par fichiers et par observations +VoteC3=merge(VoteC2,MaxI2,by.x="nom du fichier",by.y="V1") +VoteC4=merge(VoteC3,IdS3,by=c("nom du fichier","tadarida_taxon")) +VoteC4$temps_fin=as.numeric(as.character(VoteC4$temps_fin)) +VoteC4$temps_debut=as.numeric(as.character(VoteC4$temps_debut)) +VoteC4$frequence=as.numeric(as.character(VoteC4$frequence_mediane)) +VoteC4$durseq=VoteC4$temps_fin-VoteC4$temps_debut + +ProbEsp_C2b=predict(ClassifEspC2b,VoteC4,type="prob",norm.votes=TRUE) +ProbEsp_C2bs=predict(ClassifEspC2b,VoteC4,type="response",norm.votes=TRUE) + +colnum=match("participation",colnames(VoteC4)) +DataCorrC2=cbind(VoteC4[,1:colnum],ProbEsp_C2b,ProbEsp_C2bs) +DataCorrC2=DataCorrC2[order(DataCorrC2$tadarida_probabilite,decreasing=T),] +DataCorrC2=DataCorrC2[order(DataCorrC2$'nom du fichier'),] + +DataCorrC2$ProbEsp_C2bs=as.character(DataCorrC2$ProbEsp_C2bs) +DataCorrC2$ProbEsp_C2bs[is.na(DataCorrC2$ProbEsp_C2bs)]="empty" + +fout_name="output.tabular" + +write.table(DataCorrC2,file=fout_name,row.names=FALSE,sep="\t") +#write.table(DataCorrC2,paste0(substr(args[1],nchar(args[1])-40,nchar(args[1])-17),"-DataCorrC2.csv"),row.names=F,sep="\t")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/IdCorrect_2ndLayer_en.xml Mon Aug 06 09:13:29 2018 -0400 @@ -0,0 +1,102 @@ +<tool id="IdCorrect_2ndLayer" name="Tadarida data cleaner" version="0.1"> + <description>clean data from animal detection on acoustic recordings</description> + <requirements> + <requirement type="package" version="1.10.4">r-data.table</requirement> + <requirement type="package" version="4.6_12">r-randomforest</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + Rscript + '$__tool_directory__/IdCorrect_2ndLayer.R' '$participation_file' + + #if $learner.condi_learner == "custom": + '$learner.user_learner' + #else + '$__tool_directory__/ClassifEspC2b_180222.learner' + #end if + + '${participation_file.name}' + + '$output' +]]> + </command> + <inputs> + <param name="participation_file" type="data" format="csv" label="Participation file"/> + <param name="learner" type="data" label="Choose your leaner" format="rdata"/> + + <conditional name="learner"> + <param name="condi_learner" type="select" label="Select a classifier" help="Default is ClassifEspC2b_180222"> + <option value="c18">ClassifEspC2b_180222</option> + <option value="custom">Custom Classifier</option> + </param> + + <when value="c18"> + </when> + <when value="custom"> + <param name="user_learner" type="data" label="Choose your classifier" format="rdata"/> + </when> + </conditional> + + </inputs> + <outputs> + <data name="output" from_work_dir="output.tabular" format="tabular"/> + </outputs> + <tests> + <test> + <param name="participation_file" value="IdCor2Layer_Test1_obs.csv"/> + <param name="condi_learner" value="default_learner"/> + <output name="output" file="IdCor2Layer_Test1_out.tabular"/> + </test> + <test> + <param name="participation_file" value="IdCor2Layer_Test1_obs.csv"/> + <param name="condi_learner" value="custom_learner"/> + <param name="user_learner" value="ClassifEspC2b_171206.learner"/> + <output name="output" file="IdCor2Layer_Test1_out.tabular"/> + </test> + + </tests> + <help><![CDATA[ + +.. class:: infomark + +========================== +Tadarida data cleaner +========================== + +**What it does** + +This tool intend to correct ids from 1st layer of Tadarida software, and improve data output according to context (= the whole output of a sampling session). + +**Arguments** + +It should be called with 2 consecutive arguments : + +- a summary table of TadaridaC output from vigiechiro.herokuapp.com web portal. +- the 2nd layer classifier built on validated id in Vigie-Chiro database (eg : "ClassifEspC2b_180222.learner") + ]]></help> + <citations> + <citation type="bibtex"> + @article{kerbiriou2015vigie, + title={Vigie-Chiro: 9 ans de suivi des tendances des esp{\`e}ces communes}, + author={Kerbiriou, C and Julien, JF and Bas, Y and Marmet, J and Le Viol, I and Lorrilliere, R and Azam, C and Gasc, A and Lois, G}, + journal={Symbioses, nouvelle s{\'e}rie}, + number={34}, + year={2015} + } + </citation> + <citation type="bibtex"> + @inproceedings{bas2013automatic, + title={Automatic echolocation calls identification in Europe vs. Neotropics: more species does not mean more difficult}, + author={Bas, Yves and Escallon, Antoine and Ferre, Matthieu and Haquart, Alexandre and Rufray, Vincent and Disca, Thierry and Julien, Jean-Fran{\c{c}}ois} + } + </citation> + <citation type="bibtex"> + @inproceedings{kerbiriou2010long, + title={Long term trends monitoring of bats, from biodiversity indicator production to species specialization assessment}, + author={Kerbiriou, C and Bas, Y and Dufr{\^e}ne, L and Robert, A and Julien, JF}, + booktitle={24th Annual Meeting of the Society for Conservation Biology, Edmonton, Canada}, + year={2010} + } + </citation> + <citation type="doi">10.5334/jors.154</citation> +</citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/IdValid.R Mon Aug 06 09:13:29 2018 -0400 @@ -0,0 +1,180 @@ +library(data.table) + +ValidHier=function(x,y) #used to write validator id over observer id +{ + if(y==""){x}else{y} +} + +f2p <- function(x) #get date-time data from recording file names +{ + if (is.data.frame((x)[1])) {pretemps <- vector(length = nrow(x))} + op <- options(digits.secs = 3) + pretemps <- paste(substr(x, nchar(x) - 18, nchar(x)-4), ".", substr(x, nchar(x) - 2, nchar(x)), sep = "") + strptime(pretemps, "%Y%m%d_%H%M%OS",tz="UTC")-7200 +} + +args <- commandArgs(trailingOnly = TRUE) + + +#print(args) + + +#for test +#inputest=list.files("C:/Users/Yves Bas/Documents/GitHub/65MO_Galaxy-E/raw_scripts/Vigie-Chiro/output_IdCorrect_2ndLayer_input_IdValid/",full.names=T) +#for (i in 1:length(inputest)) +#{ +#args=c(inputest[i],"Referentiel_seuils_C2.csv") +#args=c("5857d56d9ebce1000ed89ea7-DataCorrC2.csv","Referentiel_seuils_C2.csv") + + + +IdCorrect=fread(args[1]) +RefSeuil=fread(args[2]) +#IdV=as.data.frame(subset(IdCorrect,select=observateur_taxon:validateur_probabilite)) + +#Step 0 :compute id score from 2nd Layer +test=match("participation",names(IdCorrect)) +IdCorrect$IdScore=apply(as.data.frame(IdCorrect)[,(test+1):(ncol(IdCorrect)-1)],MARGIN=1,FUN=max) +#compute true success probabilities according to logistic regression issued from "Referentiel_seuils" +CorrSp=match(IdCorrect$ProbEsp_C2bs,RefSeuil$Espece) +PSp=RefSeuil$Pente[CorrSp] +ISp=RefSeuil$Int[CorrSp] + +suppressWarnings(IdCorrect$IdProb<-mapply(FUN=function(w,x,y) if((!is.na(y))&(y>0)&(y<1000)) {(exp(y*w+x)/(1+exp(y*w+x)))}else{w} ,IdCorrect$IdScore,ISp,PSp)) + + + + +#Step 1 :compute id with confidence regarding a hierarchy (validator > observer) +IdCorrect$IdV=mapply(ValidHier,IdCorrect$observateur_taxon,IdCorrect$validateur_taxon) +IdCorrect$ConfV=mapply(ValidHier,IdCorrect$observateur_probabilite + ,IdCorrect$validateur_probabilite) + + +#print(paste(args[1],length(subset(IdCorrect$ConfV,IdCorrect$ConfV!="")))) + +#Step 2: Get numerictime data +suppressWarnings(IdCorrect$Session<-NULL) +suppressWarnings(IdCorrect$TimeNum<-NULL) + +if (substr(IdCorrect$`nom du fichier`[1],2,2)=="i") #for car/walk transects +{ + FileInfo=as.data.table(tstrsplit(IdCorrect$`nom du fichier`,"-")) + IdCorrect$Session=as.numeric(substr(FileInfo$V4,5,nchar(FileInfo$V4))) + TimeSec=as.data.table(tstrsplit(FileInfo$V5,"_")) + TimeSec=as.data.frame(TimeSec) + if(sum(TimeSec[,(ncol(TimeSec)-1)]!="00000")==0) #to deal with double Kaleidoscope treatments + { + print("NOMS DE FICHIERS NON CONFORMES") + print("Vous les avez probablement traiter 2 fois par Kaleidoscope") + stop("Merci de nous signaler cette erreur par mail pour correction") + }else{ + IdCorrect$TimeNum=(IdCorrect$Session*800 + +as.numeric(TimeSec[,(ncol(TimeSec)-1)]) + +as.numeric(TimeSec[,(ncol(TimeSec))])/1000) + } + +}else{ + if(substr(IdCorrect$`nom du fichier`[1],2,2)=="a") #for stationary recordings + { + DateRec=as.POSIXlt(f2p(IdCorrect$`nom du fichier`)) + Nuit=format(as.Date(DateRec-43200*(DateRec$hour<12)),format="%d/%m/%Y") + #Nuit[is.na(Nuit)]=0 + IdCorrect$Session=Nuit + IdCorrect$TimeNum=as.numeric(DateRec) + + }else{ + print("NOMS DE FICHIERS NON CONFORMES") + stop("Ils doivent commencer par Cir (routier/pedestre) ou par Car (points fixes") + } +} + + + + +#Step 3 :treat sequentially each species identified by Tadarida-C +IdExtrap=vector() #to store the id extrapolated from validations +IdC2=IdCorrect[0,] #to store data in the right order +TypeE=vector() #to store the type of extrapolation made +for (j in 1:nlevels(as.factor(IdCorrect$ProbEsp_C2bs))) +{ + IdSp=subset(IdCorrect + ,IdCorrect$ProbEsp_C2bs==levels(as.factor(IdCorrect$ProbEsp_C2bs))[j]) + if(sum(IdSp$IdV=="")==(nrow(IdSp))) #case 1 : no validation no change + { + IdC2=rbind(IdC2,IdSp) + IdExtrap=c(IdExtrap,rep(IdSp$ProbEsp_C2bs[1],nrow(IdSp))) + TypeE=c(TypeE,rep(0,nrow(IdSp))) + }else{ #case 2: some validation + Vtemp=subset(IdSp,IdSp$IdV!="") + #case2A: validations are homogeneous + if(nlevels(as.factor(Vtemp$IdV))==1) + { + IdC2=rbind(IdC2,IdSp) + IdExtrap=c(IdExtrap,rep(Vtemp$IdV[1],nrow(IdSp))) + TypeE=c(TypeE,rep(2,nrow(IdSp))) + }else{ + #case 2B: validations are heterogeneous + #case 2B1: some validations confirms the species identified by Tadarida and highest confidence are confirmed + subVT=subset(Vtemp,Vtemp$IdV==levels(as.factor(IdCorrect$ProbEsp_C2bs))[j]) + subVF=subset(Vtemp,Vtemp$IdV!=levels(as.factor(IdCorrect$ProbEsp_C2bs))[j]) + if((nrow(subVT)>0)&(max(subVT$IdProb)>max(subVF$IdProb))) + { + Vtemp=Vtemp[order(Vtemp$IdProb),] + test=(Vtemp$IdV!=Vtemp$ProbEsp_C2bs) + Fr1=max(which(test == TRUE)) #find the error with highest indices + Thr1=mean(Vtemp$IdProb[(Fr1):(Fr1+1)]) #define first threshold as the median confidence between the first error and the confirmed ID right over it + #id over this threshold are considered right + IdHC=subset(IdSp,IdSp$IdProb>Thr1) + IdC2=rbind(IdC2,IdHC) + IdExtrap=c(IdExtrap,rep(Vtemp$IdV[nrow(Vtemp)],nrow(IdHC))) + TypeE=c(TypeE,rep(2,nrow(IdHC))) + #id under this threshold are attributed to validated id closest in time + Vtemp=Vtemp[order(Vtemp$TimeNum),] + cuts <- c(-Inf, Vtemp$TimeNum[-1]-diff(Vtemp$TimeNum)/2, Inf) + CorrV=findInterval(IdSp$TimeNum, cuts) + IdE=Vtemp$IdV[CorrV] + IdEL=subset(IdE,IdSp$IdProb<=Thr1) + IdLC=subset(IdSp,IdSp$IdProb<=Thr1) + IdExtrap=c(IdExtrap,IdEL) + TypeE=c(TypeE,rep(1,length(IdEL))) + IdC2=rbind(IdC2,IdLC) + + + }else{ + #case 2B2: all validations concerns errors + #id are extrapolated on time only + Vtemp=Vtemp[order(Vtemp$TimeNum),] + cuts <- c(-Inf, Vtemp$TimeNum[-1]-diff(Vtemp$TimeNum)/2, Inf) + CorrV=findInterval(IdSp$TimeNum, cuts) + IdE=Vtemp$IdV[CorrV] + IdExtrap=c(IdExtrap,IdE) + TypeE=c(TypeE,rep(1,length(IdE))) + IdC2=rbind(IdC2,IdSp) + } + } + + + } + + +} +test1=(nrow(IdC2)==length(IdExtrap)) +test2=(nrow(IdC2)==nrow(IdCorrect)) +if((test1==F)|(test2==F)) +{ + (stop("Erreur de traitement !!!")) +} + +IdC2$IdExtrap=IdExtrap +IdC2$TypeE=TypeE + + +IdC2=IdC2[order(IdC2$IdProb,decreasing=T),] +IdC2=IdC2[order(IdC2$ConfV,decreasing=T),] +IdC2=IdC2[order(IdC2$`nom du fichier`),] +#discard duplicated species within the same files (= false positives corrected by 2nd layer) +IdC2=unique(IdC2,by=c("nom du fichier","IdExtrap")) + +write.table(IdC2,"output.tabular",row.names=F,sep="\t") +#write.table(IdC2,paste0(substr(args[1],1,nchar(args[1])-15),"-IdC2.csv"),row.names=F,sep="\t")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/IdValiden.xml Mon Aug 06 09:13:29 2018 -0400 @@ -0,0 +1,71 @@ +<tool id="IdValid" name="Tadarida identifications integration" version="0.1"> + <description>Integrate identifications from animal detection on acoustic recordings</description> + <requirements> + <requirement type="package" version="1.10.4">r-data.table</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + Rscript + '$__tool_directory__/IdValid.R' '$inputfile' '$__tool_directory__/Referentiel_seuils_C2.csv' '$output' +]]> + </command> + <inputs> + <param name="inputfile" type="data" format="tabular" label="IdCorrect 2nd layer output"/> + </inputs> + <outputs> + <data name="output" format="tabular" from_work_dir="output.tabular" label="${tool.name} on ${on_string}"/> + </outputs> + + <tests> + <test> + <param name="inputfile" value="IdCor2Layer_Test1_out.tabular"/> + <output name="output" file="BilanEnrichiPF_Test1.tabular"/> + </test> + </tests> + + + <help><![CDATA[ + +.. class:: infomark + +===================================== +Tadarida identifications integration +===================================== + +**What it does** + +This tool allows to integrate identifications made by observers and validators and will provide an input for synthesis of participations. + + +**Arguments** + +- The input is a tabular file, output from the tool IdCorrect_2ndLayer. +- The output is a single tabular file with validated Ids + + ]]></help> + <citations> + <citation type="bibtex"> + @article{kerbiriou2015vigie, + title={Vigie-Chiro: 9 ans de suivi des tendances des esp{\`e}ces communes}, + author={Kerbiriou, C and Julien, JF and Bas, Y and Marmet, J and Le Viol, I and Lorrilliere, R and Azam, C and Gasc, A and Lois, G}, + journal={Symbioses, nouvelle s{\'e}rie}, + number={34}, + year={2015} + } + </citation> + <citation type="bibtex"> + @inproceedings{bas2013automatic, + title={Automatic echolocation calls identification in Europe vs. Neotropics: more species does not mean more difficult}, + author={Bas, Yves and Escallon, Antoine and Ferre, Matthieu and Haquart, Alexandre and Rufray, Vincent and Disca, Thierry and Julien, Jean-Fran{\c{c}}ois} + } + </citation> + <citation type="bibtex"> + @inproceedings{kerbiriou2010long, + title={Long term trends monitoring of bats, from biodiversity indicator production to species specialization assessment}, + author={Kerbiriou, C and Bas, Y and Dufr{\^e}ne, L and Robert, A and Julien, JF}, + booktitle={24th Annual Meeting of the Society for Conservation Biology, Edmonton, Canada}, + year={2010} + } + </citation> + <citation type="doi">10.5334/jors.154</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Referentiel_seuils_C2.csv Mon Aug 06 09:13:29 2018 -0400 @@ -0,0 +1,77 @@ +Espece;Int;Pente;Seuil50;Seuil90;FN50;FN90;FP50;FP90;Int;Pente;Seuil50;Seuil90;FN50;FN90;FP50;FP90;Perftot;PerfP2;ratio;;PerfPFtot;Espece;FN50;FN90;FP50;FP90;Int;Pente;Seuil50;Seuil90 +chirp;-9.796506402;46.92990813;0.209;0.256;0.08;0.12;0.041666667;0;-9.56313307;44.09513566;0.217;0.267;0.08;0.08;0;0;0.060416667;0.04;0.662068966;0.662068966;0.060416667;chirp;0.08;0.12;0.041666667;0;-9.621801388;46.06782011;0.209;0.257 +Rhifer;-5.993856471;15.08754459;0.398;0.543;0.298076923;0.298076923;0.058064516;0.058064516;-5.889843127;16.57369156;0.356;0.488;0.281553398;0.296116505;0.051282051;0.052287582;0.17807072;0.170309884;0.956417115;0.99245238;0.171605094;Rhifer;0.291262136;0.291262136;0.051948052;0.051948052;-5.851562087;15.04050575;0.39;0.536 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+Ptebon;-7.104430767;-90.42057688;Inf;Inf;1;1;NaN;NaN;-6.864251121;-3122.119677;Inf;Inf;1;1;NaN;NaN;1;1;1;1;1;Ptebon;1;1;NaN;NaN;-6.909678589;-107.7304759;Inf;Inf +Pteger;-6.806622284;87.05551581;0.079;0.104;1;1;1;1;-6.626389738;84.39747813;0.079;0.105;1;1;1;1;1;1;1;1;1;Pteger;1;1;1;1;-6.671816986;87.04908905;0.077;0.102 +Sepsep;-6.572236956;44.50635929;0.148;0.198;1;1;NaN;NaN;-6.457679388;46.23209872;0.14;0.188;0.970588235;1;0;NaN;1;0.656862745;0.656862745;0.656862745;1;Sepsep;1;1;NaN;NaN;-6.413986714;41.92249556;0.153;0.206 +Tetcan;-6.224979865;31.00464875;0.201;0.272;1;1;NaN;NaN;-6.073393155;34.28510365;0.178;0.242;1;1;NaN;NaN;1;1;1;1;1;Tetcan;1;1;NaN;NaN;-6.040290768;29.26243379;0.207;0.282 +Ratnor;-7.634127214;58.5655848;0.131;0.168;1;1;1;NaN;;;;;;;;;1;#DIV/0!;#DIV/0!;#DIV/0!;#DIV/0!;;;;;;;;;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SpeciesList.csv Mon Aug 06 09:13:29 2018 -0400 @@ -0,0 +1,214 @@ +Esp;Nesp;France;Turquie;Espagne;Norfolk;Scientific name;Group;NomFR;GroupFR +Aegcau;piaf;x;x;x;x;Aegithalos caudatus;bird;Mésange à longue queue;Autre +Alcatt;piaf;x;x;x;x;Alcedo atthis;bird;Martin-pêcheur d'Europe;Autre +amph;amph;x;x;x;x;Amphibia sp.;frog;Amphibien sp.;Autre +Antius;Antius;x;;x;;Antaxius spinibrachius;bush-cricket;Antaxie voyageuse;Sauterelle +Antped;Antped;x;;;;Antaxius pedestris;bush-cricket;Antaxie marbree;Sauterelle +Antpet;piaf;x;x;;;Anthus petrosus;bird;Pipit maritime;Autre +Antsor;Antsor;x;;;;Antaxius sorrezensis;bush-cricket;Antaxie cevenole;Sauterelle +Apoagr;Aposp;x;;;;Apodemus agrarius;other mammal;Mulot rayé;Autre +Apofla;Aposp;x;x;x;;Apodemus flavicollis;other mammal;Mulot à collier;Autre +Aposp;Aposp;x;x;x;x;Apodemus sp.;other mammal;Mulot sp.;Autre +Aposyl;Aposp;x;x;x;x;Apodemus sylvaticus;other mammal;Mulot sylvestre;Autre +Apuapu;piaf;x;x;x;x;Apus apus;bird;Martinet noir;Autre +Barbar;Barbar;x;x;x;x;Barbastella barbastellus;bat;Barbastelle d'Europe;Chauve-souris +Barfis;Barfis;x;;;;Barbitistes fischeri;bush-cricket;Barbitiste languedocien;Sauterelle +Barsan;Barsan;x;;x;;Barbitistes 'sanzii';bush-cricket;Barbitiste cryptique;Sauterelle +Barser;Barser;x;;x;;Barbitistes serricauda;bush-cricket;Barbitiste des bois;Sauterelle +Bicbic;Bicbic;x;;x;;Bicolorana bicolor;bush-cricket;Decticelle bicolore;Sauterelle +buzz;noise;x;x;x;x;insect wingbeats;noise;bourdonnement;Autre +car;noise;x;x;x;x;vehicle;noise;véhicule;Autre +Carcar;piaf;x;x;x;x;Carduelis carduelis;bird;Chardonneret élégant;Autre +Cerbra;piaf;x;x;x;x;Certhia brachydactyla;bird;Grimpereau des jardins;Autre +Cetcet;piaf;x;x;x;x;Cettia cettia;bird;Bouscarle de Cetti;Autre +chirp;chirp;x;;;;chirp;noise;chirp;Autre +Chlchl;piaf;x;x;x;x;Chloris chloris;bird;Verdier d'Europe;Autre +Chovag;criq;x;x;x;x;Chorthippus vagans;grasshopper;Criquet des pins;Autre +Cicatr;Cicatr;x;x;x;;Cicadatra atra;cicada;Cigale noire;Autre +Cicorn;Cicorn;x;x;x;;Cicada orni;cicada;Cigale grise;Autre +Cisjun;piaf;x;x;x;x;Cisticola juncidis;bird;Cisticole des joncs;Autre +Concon;Concon;x;x;x;;Conocephalus conocephalus;bush-cricket;Conocéphale africain;Sauterelle +Condor;Condor;x;x;x;x;Conocephalus dorsalis;bush-cricket;Conocephale des marais;Sauterelle +Confus;Confus;x;;x;x;Conocephalus fuscus;bush-cricket;Conocephale bigarre;Sauterelle +Corcho;Epheph;x;;;;Corsteropleurus chopardi;bush-cricket;Ephippigère corse;Sauterelle +Cornix;piaf;x;x;x;x;Corvus cornix;bird;Corneille mantelée;Autre +criq;criq;x;x;x;x;Caelifera sp.;grasshopper;Criquet sp.;Autre +Crorus;Mussp;x;x;x;x;Crocidura russula;other mammal;Crocidure musette;Autre +Cyacae;piaf;x;x;x;x;Cyanistes caerulea;bird;Mésange bleue;Autre +Cympud;Cympud;x;;x;;Cymbalophora pudica;moth;Ecaille pudique;Autre +Cyrscu;Cyrscu;x;;x;;Cyrtaspis scutatus;bush-cricket;Meconeme a bouclier;Sauterelle +Decalb;Decalb;x;x;x;;Decticus albifrons;bush-cricket;Dectique a front blanc;Sauterelle +Denmaj;piaf;x;x;x;x;Dendrocopos major;bird;Pic épeiche;Autre +elec;noise;x;x;x;x;electronical noise;noise;parasite;Autre +Embcae;piaf;x;x;x;x;Emberiza caesia;bird;Bruant cendrillard;Autre +Embcal;piaf;x;x;x;x;Emberiza calandra;bird;Bruant proyer;Autre +Embcir;piaf;x;x;x;x;Emberiza cirlus;bird;Bruant zizi;Autre +Embcit;piaf;x;x;x;x;Emberiza citrinella;bird;Bruant jaune;Autre +Epheph;Epheph;x;;x;;Ephippiger ephippiger;bush-cricket;Ephippigere des vignes;Sauterelle +Eptana;Eptnil;x;x;;;Eptesicus anatolicus;bat;Serotine d'Anatolie;Chauve-souris +Eptisa;Eptisa;;;x;;Eptesicus isabellinus;bat;Serotine isabelle;Chauve-souris +Eptnil;Eptnil;x;;x;;Eptesicus nilssonii;bat;Sérotine boréale;Chauve-souris +Eptser;Eptser;x;x;x;x;Eptesicus serotinus;bat;Serotine commune;Chauve-souris +Erirub;piaf;x;x;x;x;Erithacus rubecula;bird;Rougegorge familier;Autre +Euccho;criq;x;x;x;x;Euchorthippus chopardii;grasshopper;Criquet des bragalous;Autre +Eumbor;gril;x;x;x;;Eumodycogryllus bordigalensis;ground-cricket;Grillon bordelais;Autre +Eupcha;Eupsp;x;x;;;Eupholidoptera chabrieri;bush-cricket;Decticelle splendide;Sauterelle +Eupsp;Eupsp;x;x;;;Eupholidoptera sp.;bush-cricket;Decticelle splendide;Sauterelle +Euptyr;Eupsp;x;x;x;;Eupholidoptera tyrrhenica;bush-cricket;Decticelle corse;Sauterelle +Fricoe;piaf;x;x;x;x;Fringilla coelebs;bird;Pinson des arbres;Autre +gril;gril;x;x;x;x;Gryllidae sp.;ground-cricket;grillon sp.;Autre +Grycam;gril;x;x;x;;Gryllus campestris;ground-cricket;Grillon champêtre;Autre +Homsap;mamm;x;x;x;x;Homo sapiens;other mammal;voix;Autre +Hylmer;amph;x;;x;;Hyla meridionalis;frog;Rainette méridionale;Autre +Hypsav;Hypsav;x;x;x;;Hypsugo savii;bat;Vespere de Savi;Chauve-souris +Insp10;Insp10;x;x;x;x;Insect sp.10;insect;Insecte sp. type 10;Autre +Insp11;Insp11;x;x;x;x;Insect sp.11;insect;Insecte sp. type 11;Autre +Insp12;Insp12;x;x;x;x;Insect sp.12;insect;Insecte sp. type 12;Autre +Inssp1;Inssp1;x;;x;x;Insect sp.1;insect;Insecte sp. type 1;Autre +Inssp2;Inssp2;x;;x;x;Insect sp.2;insect;Insecte sp. type 2;Autre +Inssp5;Inssp5;x;;x;x;Insect sp.5;insect;Insecte sp. type 5;Autre +Inssp6;Inssp6;x;;x;x;Insect sp.6;insect;Insecte sp. type 6;Autre +Inssp7;Inssp7;x;;x;x;Insect sp.7;insect;Insecte sp. type 7;Autre +Inssp8;Inssp8;x;x;x;x;Insect sp. 8;insect;Insecte sp. type 8;Autre +Inssp9;Inssp9;x;x;x;x;Insect sp. 9;insect;Insecte sp. type 9;Autre +InsTu1;InsTu1;;x;;;Insect sp. from Turkey 1;insect;Insecte sp. Tu1;Autre +Isopyr;Isopyr;x;x;x;;Isophya pyrenea;bush-cricket;Barbatiste pyreneen;Sauterelle +Lamsp.;Lamsp.;x;x;x;x;Lampyris sp.;beetle;Lampyre sp.;Autre +Lepalb;Lepalb;x;x;;;Leptophyes albovittata;bush-cricket;Sauterelle rayee;Sauterelle +Lepbos;Lepbos;x;;;;Leptophyes boscii;bush-cricket;Sauterelle sarmate;Sauterelle +Leppun;Leppun;x;;x;x;Leptophyes punctatissima;bush-cricket;Sauterelle ponctuee;Sauterelle +Llusta;Llusta;;;x;;Lluciapomaresius stalii;bush-cricket;Ephippigere de Stal;Sauterelle +Lopcri;piaf;x;x;x;x;Lophophanes cristatus;bird;Mésange huppée;Autre +Lusmeg;piaf;x;x;x;x;Luscinia megarhynchos;bird;Rossignol philomèle;Autre +Lyrple;Lyrple;x;x;x;;Lyristes plebejus;cicada;Cigale commune;Autre +mamm;mamm;x;x;x;x;Mammalia sp.;other mammal;Mammifere sp.;Autre +mec;noise;x;x;x;x;mechanical noise;noise;autre bruit;Autre +Metbra;Metbra;x;;;x;Metrioptera brachyptera;bush-cricket;Decticelle des bruyeres;Sauterelle +Metsau;Metsau;x;x;x;;Metrioptera saussuriana;bush-cricket;Decticelle des alpages;Sauterelle +Micagr;Micagr;x;x;x;x;Microtus agrestis;other mammal;Campagnol agreste;Autre +Minsch;Minsch;x;x;x;;Miniopterus schreibersii;bat;Minioptere;Chauve-souris +Mmasp1;mamm;x;x;x;x;micromammals sp.1;other mammal;Micromammifère type 1;Autre +Mmasp2;mamm;x;x;x;x;micromammals sp.2;other mammal;Micromammifère type 2;Autre +Mmasp3;mamm;x;x;x;x;micromammals sp.3;other mammal;Micromammifère type 3;Autre +Mmasp4;mamm;x;x;x;x;micromammals sp.4;other mammal;Micromammifère type 4;Autre +MmaTu1;mamm;x;x;x;;micromammals sp. from Turkey 1;other mammal;Micromammifère de Turquie type 1;Autre +Motcin;piaf;x;x;x;x;Motacilla cinerea;bird;Bergeronnette des ruisseaux;Autre +Motfla;piaf;x;x;x;x;Motacilla flava;bird;Bergeronnette printanière;Autre +Mussp;Mussp;x;x;x;x;Soricidae sp.;other mammal;Musaraigne sp.;Autre +Myoalc;Myoalc;x;x;x;x;Myotis alcathoe;bat;Murin d'Alcathoe;Chauve-souris +Myobec;Myobec;x;x;x;x;Myotis bechsteinii;bat;Murin de Bechstein;Chauve-souris +Myobly;MyoGT;x;x;x;;Myotis blythii;bat;Petit Murin;Chauve-souris +Myobra;Myomys;x;x;;x;Myotis brandtii;bat;Murin de Brandt;Chauve-souris +Myocap;Myocap;x;x;x;;Myotis capaccinii;bat;Murin de Capaccini;Chauve-souris +Myodas;Myodas;x;x;;;Myotis dasycneme;bat;Murin des marais;Chauve-souris +Myodau;Myodau;x;x;x;x;Myotis daubentonii;bat;Murin de Daubenton;Chauve-souris +Myoema;Myoema;x;x;x;x;Myotis emarginatus;bat;Murin a oreilles echancrees;Chauve-souris +MyoGT;MyoGT;x;x;x;x;Myotis cf. myotis;bat;Murin de grande taille;Chauve-souris +Myomyo;MyoGT;x;x;x;;Myotis myotis;bat;Grand Murin;Chauve-souris +Myomys;Myomys;x;x;x;x;Myotis mystacinus;bat;Murin a moustaches;Chauve-souris +Myonat;Myonat;x;x;;x;Myotis nattereri;bat;Murin groupe Natterer;Chauve-souris +MyospA;Myonat;x;x;x;x;Myotis sp. A ('southern' Natterer);bat;Murin sp. A;Chauve-souris +noise;noise;x;x;x;x;noise;noise;bruit;Autre +Nyclas;Nyclas;x;x;x;;Nyctalus lasiopterus;bat;Grande Noctule;Chauve-souris +Nyclei;Nyclei;x;x;x;x;Nyctalus leisleri;bat;Noctule de Leisler;Chauve-souris +Nycnoc;Nycnoc;x;x;x;x;Nyctalus noctula;bat;Noctule commune;Chauve-souris +Odomac;Odomac;;;x;;Odontura macphersoni;bush-cricket;Sauterelle de MacPherson;Sauterelle +Omovir;criq;x;x;x;x;Omocestus viridulus;grasshopper;Criquet verdelet;Autre +Oriori;piaf;x;x;x;x;Oriolus oriolus;bird;Loriot d'Europe;Autre +Ortsp.;Ortsp.;x;x;x;x;Orthoptera sp.;insect;Orthoptère sp.;Autre +Panbia;piaf;x;x;x;x;Panurus biarmicus;bird;Panure à moustaches;Autre +Parmaj;piaf;x;x;x;x;Parus major;bird;Mésange charbonnière;Autre +Pasdom;piaf;x;x;x;x;Passer domesticus;bird;Moineau domestique;Autre +Pelbed;amph;x;x;x;x;Pelophylax bedriagae;frog;Grenouille de Bedriaga;Autre +Pelesc;amph;x;;;;Pelophylax esculantus;frog;Grenouille verte;Autre +Pelgra;amph;x;;x;;Pelophylax grafi;frog;Grenouille de Graf;Autre +Pelrid;amph;x;x;x;x;Pelophylax ridibundus;frog;Grenouille rieuse;Autre +Perate;piaf;x;x;x;x;Periparus ater;bird;Mésange noire;Autre +Phafal;Phafal;x;x;x;;Phaneroptera falcata;bush-cricket;Phaneroptere commun;Sauterelle +Phanan;Phanan;x;x;x;;Phaneroptera nana;bush-cricket;Phaneroptere meridional;Sauterelle +Phofem;Phofem;x;x;;;Pholidoptera femorata;bush-cricket;Decticelle des friches;Sauterelle +Phogri;Phogri;x;x;x;x;Pholidoptera griseoaptera;bush-cricket;Decticelle cendree;Sauterelle +Phopho;piaf;x;x;x;x;Phoenicurus phoenicurus;bird;Rougequeue à front blanc;Autre +Phycol;piaf;x;x;x;x;Phylloscopus collybita;bird;Pouillot véloce;Autre +piaf;piaf;x;x;x;x;Aves sp.;bird;Oiseau sp.;Autre +Picpic;piaf;x;x;x;x;Pica pica;bird;Pie bavarde;Autre +Pipkuh;Pipkuh;x;x;x;x;Pipistrellus kuhlii;bat;Pipistrelle de Kuhl;Chauve-souris +Pipmad;Pipmad;;;;;Pipistrellus madeirensis;bat;Pipistrelle de Madère;Chauve-souris +Pipnat;Pipnat;x;x;x;x;Pipistrellus nathusii;bat;Pipistrelle de Nathusius;Chauve-souris +Pippip;Pippip;x;x;x;x;Pipistrellus pipistrellus;bat;Pipistrelle commune;Chauve-souris +Pippyg;Pippyg;x;x;x;x;Pipistrellus pygmaeus;bat;Pipistrelle soprane;Chauve-souris +Plaaff;Plaaff;x;;x;;Platycleis affinis;bush-cricket;Decticelle cotiere;Sauterelle +Plaalb;Plaalb;x;;x;x;Platycleis albopunctata;bush-cricket;Decticelle chagrinee;Sauterelle +Plafal;Plafal;x;;x;;Platycleis falx;bush-cricket;Decticelle a serpe;Sauterelle +Plaibe;Plaibe;;;x;;Platycleis iberica;bush-cricket;Decticelle iberique;Sauterelle +Plaint;Plaint;x;;x;;Platycleis intermedia;bush-cricket;Decticelle intermediaire;Sauterelle +Plasab;Plasab;x;;x;;Platycleis sabulosa;bush-cricket;Decticelle des sables;Sauterelle +Pleaur;Pleaur;x;;x;x;Plecotus auritus;bat;Oreillard roux;Chauve-souris +Pleaus;Pleaus;x;;x;x;Plecotus austriacus;bat;Oreillard gris;Chauve-souris +Plekol;Plekol;;x;;;Plecotus kolombatovici;bat;Oreillard des Balkans;Chauve-souris +Plemac;Plemac;x;x;x;;Plecotus macrobullaris;bat;Oreillard montagnard;Chauve-souris +Poepal;piaf;x;x;x;x;Poecilus palustris;bird;Mésange nonnette;Autre +Prumod;piaf;x;x;x;x;Prunella modularis;bird;Accenteur mouchet;Autre +Ptebon;Ptebon;x;;;;Pterolepis bonfilsi;bush-cricket;Decticelle d'Evisa;Sauterelle +Ptecor;Ptecor;x;;;;Pterolepis corsicana;bush-cricket;Decticelle de Porto-Vecchio;Sauterelle +Pteger;Pteger;x;x;;;Pterolepis germanica;bush-cricket;Decticelle orientale;Sauterelle +Ptegra;Ptegra;;x;x;;Pterolepis grallata;bush-cricket;Decticelle a pattes fines;Sauterelle +Ptehey;gril;x;x;x;;Pteronemobius heydenii;ground-cricket;Grillon des marais;Autre +Ptepon;Ptepon;x;x;x;;Pterolepis poneli;bush-cricket;Decticelle varoise;Sauterelle +Pycgos;piaf;x;x;x;;Pycnonotus xanthopygos;bird;Bulbul d'Arabie;Autre +Pycjug;Pycjug;;;x;;Pycnogaster jugicola;bush-cricket;Ephippigere droite;Sauterelle +rain;noise;x;x;x;x;rain;noise;pluie;Autre +Ratnor;Ratnor;x;x;x;x;Rattus norvegicus;other mammal;Surmulot;Autre +Regign;piaf;x;x;x;x;Regulus ignicapillus;bird;Roitelet triple-bandeau;Autre +Regreg;piaf;x;x;x;x;Regulus regulus;bird;Roitelet huppé;Autre +Rhibla;Rhibla;;x;;;Rhinolophus blasii;bat;Rhinolophe de Blasius;Chauve-souris +Rhieur;Rhieur;x;x;x;;Rhinolophus euryale;bat;Rhinolophe euryale;Chauve-souris +Rhifer;Rhifer;x;x;x;x;Rhinolophus ferrumequinum;bat;Grand Rhinolophe;Chauve-souris +Rhihip;Rhihip;x;x;x;x;Rhinolophus hipposideros;bat;Petit Rhinolophe;Chauve-souris +Rhimeh;Rhimeh;;x;x;;Rhinolophus mehelyi;bat;Rinolophe de Mehely;Chauve-souris +river;noise;x;x;x;x;watercourse;noise;cours d'eau;Autre +RodTu1;mamm;x;x;x;;Rodentia sp. from Turkey 1;other mammal;Rongeur de Turquie type 1;Autre +Roeroe;Roeroe;x;x;x;x;Roeseliana roeselii;bush-cricket;Decticelle bariolee;Sauterelle +Rusnit;Rusnit;x;x;x;x;Ruspolia nitidula;bush-cricket;Conocephale gracieux;Sauterelle +SauIn1;SauIn1;;;;;Tettigoniidae sp. from India 1;bush-cricket;Sauterelle sp. In1;Sauterelle +SauIn2;SauIn2;;;;;Tettigoniidae sp. from India 2;bush-cricket;Sauterelle sp. In2;Sauterelle +SauIn3;SauIn3;;;;;Tettigoniidae sp. from India 3;bush-cricket;Sauterelle sp. In3;Sauterelle +SauTu4;SauTu4;;x;;;Tettigoniidae sp. from Turkey 4;bush-cricket;Sauterelle sp. Tu4;Sauterelle +SauTu5;SauTu5;;x;;;Tettigoniidae sp. from Turkey 5;bush-cricket;Sauterelle sp. Tu5;Sauterelle +SauTu6;SauTu6;;x;;;Tettigoniidae sp. from Turkey 6;bush-cricket;Sauterelle sp. Tu6;Sauterelle +SauTu7;SauTu7;;x;;;Tettigoniidae sp. from Turkey 7;bush-cricket;Sauterelle sp. Tu7;Sauterelle +SauTurquiesp1;SauTurquiesp1;;x;;;Tettigoniidae sp. from Turkey 1;bush-cricket;Sauterelle sp. Tu1;Sauterelle +SauTurquiesp2;SauTurquiesp2;;x;;;Tettigoniidae sp. from Turkey 2;bush-cricket;Sauterelle sp. Tu2;Sauterelle +SauTurquiesp3;SauTurquiesp3;;x;;;Tettigoniidae sp. from Turkey 3;bush-cricket;Sauterelle sp. Tu3;Sauterelle +Sepsep;Sepsep;x;;x;;Sepiana sepium;bush-cricket;Decticelle echassiere;Sauterelle +Serser;piaf;x;x;x;x;Serinus serinus;bird;Serin cini;Autre +Siteur;piaf;x;x;x;x;Sitta europaea;bird;Sittelle torchepot;Autre +Sorcor;Mussp;x;x;x;x;Soricinus coronatus;bush-cricket;Musaraigne couronnée;Autre +Stralu;piaf;x;x;x;x;Strix aluco;bird;Effraie des clochers;Autre +Strdec;piaf;x;x;x;;Streptopelia decaocto;bird;Tourterelle turque;Autre +Stuvul;piaf;x;x;x;x;Sturnus vulgaris;bird;Etourneau sansonnet;Autre +Sylatr;piaf;x;x;x;x;Sylvia atricapilla;bird;Fauvette à tête noire;Autre +Sylcom;piaf;x;x;x;x;Sylvia communis;bird;Fauvette grisette;Autre +Sylmel;piaf;x;x;x;x;Sylvia melanocephala;bird;Fauvette mélanocéphale;Autre +Tadten;Tadten;x;x;x;;Tadarida teniotis;bat;Molosse;Chauve-souris +Tesori;Tesori;;;;;Tessellana orina;bush-cricket;Decticelle orina;Sauterelle +Testes;Testes;x;x;x;;Tessellana tessellata;bush-cricket;Decticelle carroyee;Sauterelle +Tetarg;Tetarg;x;;x;;Tettigetta argentata;cicada;Cigale argentee;Autre +Tetcan;Tetcan;x;x;x;;Tettigonia cantans;bush-cricket;Sauterelle cymbaliere;Sauterelle +Tethis;Tethis;;;x;;Tettigonia hispanica;bush-cricket;Sauterelle hispanique;Sauterelle +Tetpyg;Tetpyg;x;;x;;Tettigetta pygmea;cicada;Cigale pygmee;Autre +Tetvir;Tetvir;x;x;x;x;Tettigonia viridissima;bush-cricket;Sauterelle verte;Sauterelle +Thycor;Thycor;x;;x;;Thyreonotus corsicus;bush-cricket;Decticelle marocaine;Sauterelle +Trotro;piaf;x;x;x;x;Troglodytes troglodytes;bird;Troglodyte mignon;Autre +Turmer;piaf;x;x;x;x;Turdus merula;bird;Merle noir;Autre +Turphi;piaf;x;x;x;x;Turdus philomelos;bird;Grive musicienne;Autre +Tyllil;Tyllil;x;x;x;;Tylopsis lilifolia;bush-cricket;Phaneroptere liliace;Sauterelle +Urobre;Urosp;x;;;;Uromenus brevicollis;bush-cricket;Ephippigère d'Algérie;Sauterelle +Urorug;Urosp;x;;x;;Uromenus rugosicollis;bush-cricket;Ephippigere carenee;Sauterelle +Urosp;Urosp;x;x;;;Uromenus sp.;bush-cricket;Ephippigère carénée/d'Algérie;Sauterelle +Vesmur;Vesmur;x;x;x;;Vespertilio murinus;bat;Serotine bicolore;Chauve-souris +wind;noise;x;x;x;x;wind;noise;vent;Autre +Yerbey;Yerbey;x;;;;Yersinella beybienkoi;bush-cricket;Decticelle italienne;Sauterelle +Yerbey;Yerbey;x;;;;Yersinella beybienkoi;bush-cricket;Decticelle italienne;Sauterelle +Yerray;Yerray;x;;x;;Yersinella raymondii;bush-cricket;Decticelle frele;Sauterelle +Zeuabb;Zeuabb;x;;x;;Zeuneriana abbreviata;bush-cricket;Decticelle aquitaine;Sauterelle
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/refPF.csv Mon Aug 06 09:13:29 2018 -0400 @@ -0,0 +1,83 @@ +"","Espece","Q25","Q75","Q98","nbocc","DM25","DM10","DM02" +"25%","Antius","1","2","20.4","37","1507.76416134834","-264.611728382111","-1373.67915743828" +"25%","Antped","4.5","11.5","14.72","2","4808.81578743458","4051.92529139519","3648.25036017418" +"25%","Antsor","1","1","1","1","15191.5848600864","15191.5848600864","15191.5848600864" +"25%","Barbar","2","17","303.98","2102","3664.81756293774","2332.18326377869","1113.65489628792" +"25%","Barfis","1","1","1","3","6365.93376266956","4838.54704384803","4023.94079380989" +"25%","Bicbic","1.5","2.5","2.96","2","10996.9584002495","10901.6431913852","10850.8084133243" +"25%","chirp","34.75","50.25","57.38","2","-1080.94990348816","-1080.94990348816","-1080.94990348816" +"25%","Cicorn","1","2.75","3.82","10","-144.126234710217","-601.744369745255","-735.611527109146" +"25%","Condor","1","1","1","2","5638.88746488095","5109.16003108025","4826.63873305321" +"25%","Confus","1","9.5","143.36","135","803.39968407154","-464.592767357826","-1264.27222914219" +"25%","criq","1","1","1","2","749.71511721611","717.207648897171","699.870332460404" +"25%","Cympud","1","10","205.84","1159","2049.57697588206","-108.215761780739","-1468.71151192665" +"25%","Cyrscu","1","2","16.54","40","1990.10920786858","-64.0679782867432","-629.767778863907" +"25%","Decalb","1","3","9.1","20","451.158402323722","-169.394851446152","-1211.11368044853" +"25%","Epheph","1","13","120.24","179","3024.1285866499","516.397881603242","-1570.94668524743" +"25%","Eptser","2","10","110","2690","2509.24711275101","1584.50247135162","754.495276994705" +"25%","Eumbor","2.25","4.75","5.9","2","377.283349037171","234.136240005494","157.791115188599" +"25%","Eupcha","5.25","9.75","11.82","2","8215.7333689332","8009.95518920422","7900.20682668209" +"25%","Hypsav","1","9","103.1","1116","2248.41059011221","1301.39321923256","348.390803813934" +"25%","Inssp1","1","1","1","1","12292.344350338","12292.344350338","12292.344350338" +"25%","Inssp5","1","1","1.86","8","-728.431448936463","-782.042838144303","-823.320345506668" +"25%","Inssp6","1","5","40.1199999999999","500","2424.97865229845","914.47767071724","-1035.51150548935" +"25%","Isopyr","8","22","28.44","2","532.886808037758","368.638544750213","281.039470996856" +"25%","Lamsp.","1","3.75","47.98","702","2166.80326139927","844.690763473511","-947.457581233978" +"25%","Lepbos","2","2","2","1","19698.1210539341","19698.1210539341","19698.1210539341" +"25%","Leppun","41.25","1103","4140.86","990","1104.83912658691","-249.540919065476","-1406.85371873856" +"25%","mamm","1","1","2.7","16","6183.96875983477","10.0895879268645","-278.111182951928" +"25%","Micagr","1","1.5","13","47","2238.36066246033","530.938663005829","-16.9136964130399" +"25%","Minsch","1","6","130.5","826","4206.91477686167","3004.16962945461","1585.87503230571" +"25%","Mussp","1","1","1","1","1104.1836810112","1104.1836810112","1104.1836810112" +"25%","Myoalc","1","2.25","14.5999999999999","92","4125.00926113128","2734.64635419845","1854.23125097752" +"25%","Myobec","2","2","2.92","5","4397.38848257065","3523.56983032227","3057.5332157898" +"25%","Myobra","5","5","5","1","3503.78706097603","3503.78706097603","3503.78706097603" +"25%","Myocap","1","6","94.6199999999999","104","2953.33067560195","2095.68971920014","1288.69886338711" +"25%","Myodas","3.5","4.5","4.96","2","3451.95404314995","2941.47309875488","2669.21659507751" +"25%","Myodau","1","6","350.199999999996","2395","3523.05388474465","2357.6486802578","1277.44239184379" +"25%","Myoema","1","3","38.5999999999997","1035","4239.00043714046","2483.71984658241","1362.43170207977" +"25%","MyoGT","1","3","17.22","1040","4136.37232673169","2922.0745616436","1497.44925053597" +"25%","Myomys","1","4","37.14","444","4504.9568271041","2929.1723464489","1807.60458549976" +"25%","Myonat","1","6.75","52.2399999999998","2070","4100.53462767601","2735.82784142494","1745.14204066753" +"25%","noise","609","3111.25","7235.92","5060","-1766.10768318176","-1789.97119259834","-1797.40886205673" +"25%","Nyclas","1","5.5","38.68","7","1502.60388588905","1177.01388425827","887.68234380722" +"25%","Nyclei","2","14","174.68","2780","2101.66658043861","969.221526432037","-496.86254527092" +"25%","Nycnoc","1","6","123","950","1175.58238327503","418.189396619797","-994.488390636444" +"25%","Phafal","1","5","31.12","145","2818.22321665287","1387.89198203087","-1076.0002751255" +"25%","Phanan","5","196.75","1286.22","1390","-461.121517419815","-1228.30023024082","-1652.31356955051" +"25%","Phofem","1","2.5","49.7200000000001","39","2068.41903162003","-273.422169017792","-1017.87503848076" +"25%","Phogri","2","36","300","133","3167.28623771667","1046.13571507931","-124.318460326194" +"25%","piaf","10","121","771.199999999999","4681","-1486.967471838","-1711.17241072654","-1787.89137840271" +"25%","Pipkuh","7","89","1436","4189","1559.32718348503","1060.77260088921","357.113767185211" +"25%","Pipnat","1","5","45","1635","3598.21611785888","2652.12113056183","1204.36025017738" +"25%","Pippip","22","314.5","2862.8","4663","944.2108066082","285.986425304413","-682.368085184098" +"25%","Pippyg","2","56","1870.14","1850","1208.85102796555","491.482502508163","-473.14840514183" +"25%","Plaaff","2","39","518.399999999999","961","1186.96142053604","-579.112753868103","-1549.82554960251" +"25%","Plaalb","2","61.5","935.440000000002","1055","1016.66383886337","-568.569532346726","-1470.19973935128" +"25%","Plafal","1.25","1.75","1.98","2","4582.26300436258","2749.75668113232","1772.41997540951" +"25%","Plaint","2","119","2593.2","2231","242.273566842079","-900.83824698925","-1540.14236267566" +"25%","Plasab","1","10","339.76","455","1074.20996451378","-387.740073204041","-1394.40862154961" +"25%","Pleaur","1","1","4.76","63","4323.55943703652","2738.44387030601","1156.0819111824" +"25%","Pleaus","1","4","29","2122","3952.17004132271","2637.71873641015","1691.51609820366" +"25%","Plemac","3","3","3","1","1603.93373608589","1603.93373608589","1603.93373608589" +"25%","Pteger","1","8","104.16","624","1705.30042260885","258.537321424484","-1053.9468501854" +"25%","Ptepon","1","14","185.38","222","1737.58781033754","289.659371685982","-1012.17030680656" +"25%","Ratnor","1","1.25","1.94","4","6653.59038341046","6487.00690498352","6398.16238315582" +"25%","Rhieur","1","2.25","2.94","4","7479.47543311119","5479.32757034302","4412.58204353332" +"25%","Rhifer","1","7","112.68","967","2878.50191009045","1543.43428068161","-210.073269786834" +"25%","Rhihip","1","5","198.78","762","2793.44169855118","1538.45808842182","-72.6952844524384" +"25%","Roeroe","1","5","101.56","507","1533.86711502075","-419.310067510605","-1536.84663165092" +"25%","Rusnit","1","18.25","2461.22","2128","1446.99894690514","-318.348206520081","-1535.67664027214" +"25%","Sepsep","1","12","209.56","670","1171.77852892875","-410.145421075821","-1551.93597637176" +"25%","Tadten","1","6","159.48","1165","2972.54510653019","1141.22549757958","-718.695039167404" +"25%","Testes","2","61","3929.2","2681","856.26694393158","-589.754028081894","-1536.27879407883" +"25%","Tetarg","1","1","1","1","1427.14018034935","1427.14018034935","1427.14018034935" +"25%","Tetcan","2.5","4.5","4.96","3","-498.833418250084","-1007.41270055771","-1278.65498445511" +"25%","Tetpyg","1","1","6.08","33","5812.14534193277","3825.1769472599","691.60439749718" +"25%","Tetvir","10","915.25","3517.03999999999","4510","-1245.37617117166","-1635.96713280678","-1767.07428184033" +"25%","Thycor","1","1.5","2.88","4","3827.87814813852","3648.21886131763","3552.40057501316" +"25%","Tyllil","1","2","9.2","21","2519.41863942146","1398.31712245941","134.294110488891" +"25%","Urorug","1","29","1204.6","1655","812.486474514008","-663.041796922684","-1598.88818309784" +"25%","Vesmur","1","2","11","6","3089.2149399519","2337.44215130806","1811.89018826484" +"25%","Yerray","2","26","1198.96","1822","1648.10248410702","335.5679915905","-1230.61568079949" +"25%","Zeuabb","1","1","1","1","12984.534954071","12984.534954071","12984.534954071"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/refRPSeuil50.csv Mon Aug 06 09:13:29 2018 -0400 @@ -0,0 +1,28 @@ +Espece,Q25RE,Q75RE,Q98RE,nboccRE,Q25cRE,Q75cRE,Q98cRE,nbocccRE,Q25RD,Q75RD,Q98RD,nboccRD,Q25cRD,Q75cRD,Q98cRD,nbocccRD,Q25PE,Q75PE,Q98PE,nboccPE,Q25cPE,Q75cPE,Q98cPE,nbocccPE,Q25PD,Q75PD,Q98PD,nboccPD,Q25cPD,Q75cPD,Q98cPD,nbocccPD +Barbar,1,1,2.3,36,1,1,3,33,1,2,5,283,1,3,7.29999999999998,186,1,2.25,8.5,16,1,2,9.48,14,1,2,7.48,77,1,3.25,8,60 +Confus,1,1,2.07999999999998,147,1,2,5.02,100,1,2,4.88,457,1,4,12.16,222,1,3,6.2,46,1,3.5,8.32,35,1,5,24.2,89,1,7,42.8,56 +Epheph,1,2,6.52,75,1,1.75,25,50,1,2,7.42000000000002,430,1,4,20,200,1,1,4,52,1,2,6,42,1,3,16.1,196,1,5,23.36,117 +Eptser,1,2,7,898,1,4,17,472,1,4,16,1732,3,15,53.6,521,1,3.5,13.32,135,1,5.5,29.76,79,1,5,25.6,261,2,10,59.28,127 +Leppun,1,1,4,410,1,3,19.18,192,1,3,10,1183,2,10,44,305,1,3,11.08,99,1,7.25,28.6,48,2,8,32.9,406,3,24,114.36,128 +Minsch,1,1,3,301,1,2,5,222,1,2,6,28,1,4.25,13.78,12,1,2,9,115,1,4,11,78,1,4,6.68,9,1,5.5,11.4,6 +Myodau,1,1,3.18,42,1,2,4.28,37,1,1,3,224,1,2,5,166,1,4.75,21,86,1,5,36.6,61,1,6.25,33.94,204,2,12,57,111 +MyoGT,1,1,4,473,1,2,7,329,1,1,3,322,1,2,6.53999999999999,224,1,2,7.51999999999998,82,1,3,11.44,65,1,2,4.59999999999999,71,1,2,6.75999999999999,57 +noise,47,66,96,12233,457,650,882.08,1250,56,70,98,11263,563,690,921,1151,23,72,79,4490,259.75,661.5,770.24,474,64,73,85,3994,580,728,813.86,420 +Nyclei,1,1,4,29,1,2,4.6,21,1,2,7,571,1,4,14.78,312,1,2.25,27.1,16,1,2.5,33.3,12,1,3,14.72,115,1,4,27.68,75 +Nycnoc,1,2,3.92,55,1,3,12,33,1,2,6,272,1,4,13.68,159,1,1.25,13.78,12,1,2,14.84,9,1,3,16.6,71,1,3.5,36,51 +Phanan,1,1,3,34,1,3,7.28,19,1,2,9.20000000000005,541,1,5,36.56,212,1,4,22.84,17,1,3,30.6,13,1,7,35,322,1,18.5,97.92,128 +Phogri,1,1,3,526,1,2,8.07999999999998,297,1,1,3.35999999999999,233,1,2,5.68000000000001,167,1,2,11,287,1,5,26.22,140,1,5,26,240,1,13.75,58.9,106 +Pipkuh,1,3,7,3067,2,10,26,876,1,5,17.7799999999997,2762,4,31,82.8399999999999,555,1,5,27.22,890,3,17,59.5999999999997,318,1,5,49.36,783,3,20,114.02,262 +Pipnat,1,1,4,26,1,1.5,8.48,19,1,1,3,291,1,2,5,211,1,1.5,3.8,31,1,2,5,26,1,2,10.52,175,1,3,19.78,112 +Pippip,1,4,12,5675,5,24,67,1033,1,6,18,4155,10,41,106.46,628,2,11,49,1568,6,51,135.88,404,2,14,55.5999999999999,1671,13.5,80,196.56,323 +Pippyg,1,2,6.52000000000001,88,1,2.75,21.9,58,1,1,5.77999999999998,30,1,1,9.6,25,1,3,34.8000000000001,81,1,3,51.22,50,1,5,55.32,47,1,4.5,110.72,27 +Plaalb,1,2,9,261,1,2,13,165,1,2,5,488,1,4,16,210,1,4.25,15.68,84,1,6.5,26.94,54,1,7.5,44,103,2,15.75,49.72,58 +Plaint,1,2.25,22.22,340,1,2,91.0000000000003,161,1,3,11,1270,2,8,47,366,1,4,24.1999999999999,117,1,5,28.7,66,1,6,47.74,364,2,14,109.4,148 +Plasab,1,1,3.7,16,1,2,4.76,13,1,1,2.52,75,1,2,4,53,1,1.5,3.76,7,1,1.5,3.76,7,1,4,34.78,20,1,6.25,35.54,18 +Pleaus,1,1,2,59,1,1,2,57,1,2,3,280,1,2,5,209,1,2,4.02,50,1,3,5,46,1,2,5,155,1,3,8,109 +Roeroe,1,1,1.42,30,1,1,1.42,30,1,1,2,26,1,1.25,2,24,2,2,3.8,6,2,2,3.8,6,1,2,5.28,13,1,2,5.34,12 +Rusnit,2,7,24.4200000000001,2430,4,46,128.36,448,3,14,47,2871,6,91,282.38,488,2,21,66.6,221,3.25,59,155.04,82,2,47,73,242,1,105.5,312.2,91 +Sepsep,1,1,1,7,1,2.25,2.94,4,1,1,3,37,1,2,4,29,1,1,1,1,1,1,1,1,1,3.75,7.66,18,1.5,4,7.74,14 +Testes,1,2,10.66,118,1,2.5,22.6,71,1,6,22,1692,3,29.5,113,371,1,11.5,71,51,1,5.75,286.32,30,1,8,62.04,275,1,24,141.08,113 +Tetvir,1,2,13,1252,1,6,55.6,423,2,12,37.2600000000002,5988,5,73,285,949,1,6,70,440,1,9,178.6,177,2,36.5,73,1703,8,165.5,391,339 +Yerray,1,2,3,33,1,2,10.32,22,1,2,6.08,24,1,10,16.44,8,1,1,1,5,1,1.25,1.94,4,1,2,8.40000000000001,11,1,3.25,13.9,6