Mercurial > repos > ecology > vigiechiro_bilanenrichirp
changeset 0:c55e09a8b4c8 draft
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
| author | ecology |
|---|---|
| date | Wed, 13 Mar 2019 11:17:44 -0400 |
| parents | |
| children | be4e28da3919 |
| files | BilanEnrichiRP.R BilanEnrichiRPen.xml SpeciesList.csv refRPSeuil50.csv test-data/BilanEnrichiRP_Test1.tabular test-data/BilanEnrichiRP_Test1_out_tab.tabular vigiechiro_macros.xml |
| diffstat | 7 files changed, 1939 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BilanEnrichiRP.R Wed Mar 13 11:17:44 2019 -0400 @@ -0,0 +1,220 @@ +suppressMessages(library(data.table)) +suppressMessages(library(DT)) +suppressMessages(library(htmlwidgets)) + +args <- commandArgs(trailingOnly = TRUE) +EchelleErreur=c("NA","POSSIBLE","PROBABLE","SUR") +EchelleNumErreur=c(99,50,10,1) + + +IdC2=fread(args[1]) +refRP=fread(args[2]) +GroupList=fread(args[3]) + + +if(substr(IdC2$`nom du fichier`[1],2,2)!="i") +{ + stop("Protocole non conforme, ce script doit etre lance pour un protocole Routier ou Pedestre",call.=FALSE) +} + +Routier=grepl("-",substr(IdC2$`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,na.rm=TRUE) + +#compute number of files validated per species +FichValid=aggregate(IdC2$IdV,by=list(IdC2$IdExtrap,IdC2$'nom du fichier') + ,FUN=function(x) sum(!is.na(x))) +NbValid2=aggregate(FichValid$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$IdProb),] + IdSpV=subset(IdSp,!is.na(IdSp$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,!is.na(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$GroupFR,IndexGroupe) +SummPart=SummPart[with(SummPart + ,order(IndexSumm,as.numeric(Contacts_Direct),as.numeric(Contacts_Expansion),decreasing=T)),] +colnames(SummPart)=c("Code","Groupe","Nom francais","Nom scientifique" + ,"Risque d'erreur (%)","Nb Validations" + ,"Effort de validation","Nb de Contacts en expansion" + ,"Niveau d'Activite en expansion" + ,"Nb de Contacts en direct" + ,"Niveau d'Activite en direct","TriGroupe") + +#to do: extend colors to other columns to improve readability +SummHTML=datatable(SummPart, rownames = FALSE) %>% + formatStyle(columns = c("Code","Groupe","Nom francais","Nom scientifique","Risque d'erreur (%)"),valueColumns="Risque d'erreur (%)", + background = styleInterval(c(1, 10, 50), c("white", "khaki", "orange", "orangered"))) %>% + formatStyle(columns = "Effort de validation", + background = styleEqual(c("-","FAIBLE","SUFFISANT","FORT"), c("white", "cyan", "royalblue", "darkblue"))) %>% + formatStyle(columns = c("Nb de Contacts en expansion","Niveau d'Activite en expansion"),valueColumns="Niveau d'Activite en expansion", + background = styleEqual(c("FAIBLE","MODEREE","FORTE","TRES FORTE"), c("palegoldenrod", "greenyellow", "limegreen", "darkgreen"))) %>% + formatStyle(columns = c("Nb de Contacts en direct","Niveau d'Activite en direct"),valueColumns="Niveau d'Activite en direct", + background = styleEqual(c("FAIBLE","MODEREE","FORTE","TRES FORTE"), c("palegoldenrod", "greenyellow", "limegreen", "darkgreen"))) + + +saveWidget(SummHTML,"output-summaryRP.html") +write.table(SummPart,"output-summaryRP.tabular",row.names=F,sep="\t",quote=FALSE) + +#summary for each point/transect + +#compute number of files validated per species +IdC2M$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$x, probs = seq(.05, .95, .05), na.rm = TRUE)-1 +clrs <- round(seq(255, 40, length.out = length(brks) + 1), 0) %>% +{paste0("rgb(255,", ., ",", ., ")")} + + +#to do: extend colors to other columns to improve readability +SummHTMLT=datatable(SummPartTron, rownames = FALSE) %>% + formatStyle(columns = c("Code","Groupe","Nom francais","Nom scientifique","Risque d'erreur (%)"),valueColumns="Risque d'erreur (%)", + background = styleInterval(c(1, 10, 50), c("white", "khaki", "orange", "orangered"))) %>% + formatStyle(columns=ListSession, backgroundColor = styleInterval(brks, clrs)) + +saveWidget(SummHTMLT,"output-detailRP.html") +write.table(SummPartTron,"output-detailRP.tabular",row.names=F,sep="\t",quote=FALSE)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BilanEnrichiRPen.xml Wed Mar 13 11:17:44 2019 -0400 @@ -0,0 +1,56 @@ +<tool id="vigiechiro_bilanenrichirp" name="Advanced restitution: 'Routier'or 'Pedestre' protocols" version="@VERSION@"> + <description>from Animal Detection on Acoustic Recordings</description> + <macros> + <import>vigiechiro_macros.xml</import> + </macros> + <expand macro="vigiechiro_bilanPF_bilanRP_requirements"/> + <command detect_errors="exit_code"><![CDATA[ + Rscript '$__tool_directory__/BilanEnrichiRP.R' + '$idc2' + '$__tool_directory__/refRPSeuil50.csv' + '$__tool_directory__/SpeciesList.csv' + && + tail -n +2 output-summaryRP.html > tmp && mv tmp output-summaryRP.html && + tail -n +2 output-detailRP.html > tmp && mv tmp output-detailRP.html +]]> + </command> + <inputs> + <param name="idc2" type="data" format="tabular" label="Corrected and validated observation file" help="Use output file from 'Tadarida identifications integration' : a sampling session file corrected and validated. Routier or Pedestre protocol"/> + <param name="output_choice" type="select" label="Select a summarised or detailed display" multiple="true" optional="false" help="Chose whether your want a summarised or detailed display"> + <option value="detailed" selected="true">detailed output</option> + <option value="summarised">summarised output</option> + </param> + </inputs> + <outputs> + <data name="output_summary_tabular" format="tabular" from_work_dir="output-summaryRP.tabular" label="${tool.name} on ${on_string} Summary table"> + <filter>'summarised' in output_choice</filter> + </data> + <data name="output_summary_html" format="html" from_work_dir="output-summaryRP.html" label="${tool.name} on ${on_string} Summary html"> + <filter>'summarised' in output_choice</filter> + </data> + <data name="output_detail_tabular" format="tabular" from_work_dir="output-detailRP.tabular" label="${tool.name} on ${on_string} Detail table"> + <filter>'detailed' in output_choice</filter> + </data> + <data name="output_detail_html" format="html" from_work_dir="output-detailRP.html" label="${tool.name} on ${on_string} Detail html"> + <filter>'detailed' in output_choice</filter> + </data> + </outputs> + <tests> + <test> + <param name="idc2" value="BilanEnrichiRP_Test1.tabular"/> + <param name="output_choice" value="detailed"/> + <output name="output_detail_tabular" file="BilanEnrichiRP_Test1_out_tab.tabular" ftype="tabular"/> + </test> + </tests> + <help><![CDATA[ +**What it does** + +The tool analyzes the observations made with the "Routier" or "Pedestre" protocols. + +**Arguments** + +- Input is an observation/participation file corrected by the tools Tadarida data cleaner and Tadarida identifications integration. +- Outputs are Summary and details raw tabulars, and html visualisations. + ]]></help> + <expand macro="vigiechiro_bibref" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SpeciesList.csv Wed Mar 13 11:17:44 2019 -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/refRPSeuil50.csv Wed Mar 13 11:17:44 2019 -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/BilanEnrichiRP_Test1.tabular Wed Mar 13 11:17:44 2019 -0400 @@ -0,0 +1,1376 @@ +nom du fichier tadarida_taxon temps_debut temps_fin frequence_mediane tadarida_probabilite tadarida_taxon_autre observateur_taxon observateur_probabilite validateur_taxon validateur_probabilite participation amph Antius Antped Antsor Aposp Barbar Barfis Barsan Barser Bicbic chirp Cicatr Cicorn Concon Confus Corcho criq Cympud Cyrscu Decalb Epheph Eptnil Eptser Eupsp gril Hypsav Insp11 Insp12 Inssp5 Inssp6 Inssp7 Inssp8 Inssp9 Isopyr Lamsp. Leppun Lyrple mamm Metsau Micagr Minsch Mussp Myoalc Myobec Myobra Myocap Myodas Myodau Myoema MyoGT Myomys Myonat noise Nyclas Nyclei Nycnoc Ortsp. 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