| Next changeset 1:be4e28da3919 (2019-04-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa |
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added:
BilanEnrichiRP.R BilanEnrichiRPen.xml SpeciesList.csv refRPSeuil50.csv test-data/BilanEnrichiRP_Test1.tabular test-data/BilanEnrichiRP_Test1_out_tab.tabular vigiechiro_macros.xml |
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| diff -r 000000000000 -r c55e09a8b4c8 BilanEnrichiRP.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BilanEnrichiRP.R Wed Mar 13 11:17:44 2019 -0400 |
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| b'@@ -0,0 +1,220 @@\n+suppressMessages(library(data.table))\n+suppressMessages(library(DT))\n+suppressMessages(library(htmlwidgets))\n+\n+args <- commandArgs(trailingOnly = TRUE)\n+EchelleErreur=c("NA","POSSIBLE","PROBABLE","SUR")\n+EchelleNumErreur=c(99,50,10,1)\n+\n+ \n+IdC2=fread(args[1])\n+refRP=fread(args[2])\n+GroupList=fread(args[3])\n+\n+\n+if(substr(IdC2$`nom du fichier`[1],2,2)!="i")\n+{\n+ stop("Protocole non conforme, ce script doit etre lance pour un protocole Routier ou Pedestre",call.=FALSE)\n+}\n+ \n+Routier=grepl("-",substr(IdC2$`nom du fichier`[1],4,7))\n+#compute error risk by species (minimum error among files)\n+#to be replaced by glm outputs if I\'ll have time\n+RisqueErreurT=aggregate(IdC2$IdProb,by=list(IdC2$IdExtrap),FUN=function(x) ceiling((1-max(x-0.0001))*100))\n+#barplot(RisqueErreurT$x,names.arg=RisqueErreurT$Group.1,las=2)\n+#compute error risk accoring to observer/validator (a little dirty because it relies on alphabetical order of confidence classes: POSSIBLE < PROBABLE < SUR)\n+RisqueErreurOV0=match(IdC2$ConfV,EchelleErreur)\n+RisqueErreurOV=aggregate(RisqueErreurOV0,by=list(IdC2$IdExtrap)\n+ ,FUN=max) \n+RisqueErreurOV2=EchelleNumErreur[RisqueErreurOV$x]\n+#compute minimum error risk between man and machine\n+RisqueErreur=pmin(RisqueErreurT$x,RisqueErreurOV2,na.rm=TRUE)\n+\n+#compute number of files validated per species\n+FichValid=aggregate(IdC2$IdV,by=list(IdC2$IdExtrap,IdC2$\'nom du fichier\')\n+ ,FUN=function(x) sum(!is.na(x))) \n+NbValid2=aggregate(FichValid$x,by=list(FichValid$Group.1),FUN=function(x) sum(x>0))\n+\n+DiffC50=vector() # to store the median of confidence difference between unvalidated records and validated ones\n+DiffT50=vector() # to store the median of time difference between unvalidated records and validated ones\n+for (j in 1:nlevels(as.factor(IdC2$IdExtrap)))\n+{\n+ IdSp=subset(IdC2\n+ ,IdC2$IdExtrap==levels(as.factor(IdC2$IdExtrap))[j])\n+ IdSp$IdProb[is.na(IdSp$IdProb)]=0\n+ IdSp=IdSp[order(IdSp$IdProb),]\n+ IdSpV=subset(IdSp,!is.na(IdSp$IdV))\n+ if(nrow(IdSpV)>0)\n+ {\n+ cuts <- c(-Inf, IdSpV$IdProb[-1]-diff(IdSpV$IdProb)/2, Inf)\n+ CorrC=findInterval(IdSp$IdProb, cuts)\n+ CorrC2=IdSpV$IdProb[CorrC]\n+ DiffC=abs(IdSp$IdProb-CorrC2)\n+ DiffC50=c(DiffC50,median(DiffC))\n+ \n+ IdSp=IdSp[order(IdSp$TimeNum),]\n+ IdSpV=subset(IdSp,!is.na(IdSp$IdV))\n+ cuts <- c(-Inf, IdSpV$TimeNum[-1]-diff(IdSpV$TimeNum)/2, Inf)\n+ CorrT=findInterval(IdSp$TimeNum, cuts)\n+ CorrT2=IdSpV$TimeNum[CorrT]\n+ DiffT=abs(IdSp$TimeNum-CorrT2)\n+ DiffT50=c(DiffT50,median(DiffT))\n+ }else{\n+ DiffC50=c(DiffC50,Inf)\n+ DiffT50=c(DiffT50,Inf)\n+ }\n+}\n+#compute an index of validation effort per species\n+EffortV=1/DiffC50/DiffT50\n+EffortClass=(EffortV>0.0005)+(EffortV>0.005)+RisqueErreurOV$x\n+#cbind(RisqueErreurOV,EffortV,DiffC50,DiffT50)\n+#barplot(EffortClass-1,names.arg=NbValid2$Group.1,las=2)\n+ClassEffortV=c("-","FAIBLE","SUFFISANT","SUFFISANT","FORT","FORT")\n+EffortClassMot=ClassEffortV[EffortClass]\n+\n+\n+#compare activity / reference frame\n+FileInfo=as.data.table(tstrsplit(IdC2$`nom du fichier`,"-"))\n+IdC2$Tron=FileInfo$V4\n+\n+MicTempsInfo=as.data.table(tstrsplit(as.data.frame(FileInfo)[,(ncol(FileInfo))],"_"))\n+MicDroit=(as.data.frame(MicTempsInfo)[,(ncol(MicTempsInfo)-2)]=="1")\n+IdC2$MicDroit=MicDroit\n+\n+testTempsFin=aggregate(IdC2$temps_fin,by=list(MicDroit),FUN=max)\n+testTempsFin$Direct=(testTempsFin$x>0.5)\n+testTF2=sum((testTempsFin$x>0.5))\n+if(testTF2>1){stop("Probleme stereo : les 2 canaux semblent etre en enregistrement direct")}\n+IdC2M=merge(IdC2,testTempsFin,by.x="MicDroit",by.y="Group.1")\n+\n+ActMoy=aggregate(IdC2$`nom du fichier`\n+ ,by=list(IdC2M$IdExtrap,IdC2M$Direct),FUN=length)\n+ListSpref=match(levels(as.factor(ActMoy$Group.1)),refRP$Espece)\n+Subref=refRP[ListSpref]\n+if(Routier)\n+{\n+ Subref=Subref[,c(1:17)]\n+}else{\n+ Subref=Subref[,c(1,18:33)]\n+}\n+QualifActE=vector()\n+QualifActD=vector()\n+\n+for (k in 1:nlevels(as.factor(ActMoy$Group.1)'..b'd2$x,EffortValid=EffortClassMot)\n+\n+test=match("FALSE",colnames(ActED))\n+if(is.na(test)==F)\n+{\n+ SummPart0=cbind(SummPart0,Contacts_Expansion=ActED$\'FALSE\'\n+ ,Niveau_Activite_Expansion=QualifActMotE)\n+}else{\n+ SummPart0=cbind(SummPart0,Contacts_Expansion=""\n+ ,Niveau_Activite_Expansion="")\n+}\n+test=match("TRUE",colnames(ActED))\n+if(is.na(test)==F)\n+{\n+ \n+ SummPart0=cbind(SummPart0,Contacts_Direct=ActED$\'TRUE\'\n+ ,Niveau_Activite_Direct=QualifActMotD)\n+}else{\n+ SummPart0=cbind(SummPart0,Contacts_Direct=""\n+ ,Niveau_Activite_Direct="")\n+}\n+\n+InfoSp=c("GroupFR","NomFR","Scientific name","Esp")\n+GroupShort=GroupList[,..InfoSp]\n+SummPart=merge(GroupShort,SummPart0,by="Esp")\n+IndexGroupe=c("Autre","Sauterelle","Chauve-souris")\n+SummPart$IndexSumm=match(SummPart$GroupFR,IndexGroupe)\n+SummPart=SummPart[with(SummPart\n+ ,order(IndexSumm,as.numeric(Contacts_Direct),as.numeric(Contacts_Expansion),decreasing=T)),]\n+colnames(SummPart)=c("Code","Groupe","Nom francais","Nom scientifique"\n+ ,"Risque d\'erreur (%)","Nb Validations"\n+ ,"Effort de validation","Nb de Contacts en expansion"\n+ ,"Niveau d\'Activite en expansion"\n+ ,"Nb de Contacts en direct"\n+ ,"Niveau d\'Activite en direct","TriGroupe")\n+\n+#to do: extend colors to other columns to improve readability\n+SummHTML=datatable(SummPart, rownames = FALSE) %>%\n+ formatStyle(columns = c("Code","Groupe","Nom francais","Nom scientifique","Risque d\'erreur (%)"),valueColumns="Risque d\'erreur (%)", \n+ background = styleInterval(c(1, 10, 50), c("white", "khaki", "orange", "orangered"))) %>%\n+ formatStyle(columns = "Effort de validation", \n+ background = styleEqual(c("-","FAIBLE","SUFFISANT","FORT"), c("white", "cyan", "royalblue", "darkblue"))) %>%\n+ formatStyle(columns = c("Nb de Contacts en expansion","Niveau d\'Activite en expansion"),valueColumns="Niveau d\'Activite en expansion", \n+ background = styleEqual(c("FAIBLE","MODEREE","FORTE","TRES FORTE"), c("palegoldenrod", "greenyellow", "limegreen", "darkgreen"))) %>%\n+ formatStyle(columns = c("Nb de Contacts en direct","Niveau d\'Activite en direct"),valueColumns="Niveau d\'Activite en direct", \n+ background = styleEqual(c("FAIBLE","MODEREE","FORTE","TRES FORTE"), c("palegoldenrod", "greenyellow", "limegreen", "darkgreen")))\n+\n+\n+saveWidget(SummHTML,"output-summaryRP.html")\n+write.table(SummPart,"output-summaryRP.tabular",row.names=F,sep="\\t",quote=FALSE)\n+\n+#summary for each point/transect\n+\n+#compute number of files validated per species\n+IdC2M$Canal=sapply(IdC2M$Direct,FUN=function(x) if(x){"Direct"}else{"Expansion"})\n+\n+ActMoyTA=aggregate(IdC2M$`nom du fichier`,by=list(IdC2M$IdExtrap,IdC2M$Canal,IdC2M$Session),FUN=length)\n+ActMoyT=dcast(data=IdC2M,formula=IdExtrap+Canal~Session\n+ ,fun.aggregate=length)\n+SummPartshort=cbind(SummPart[,c(1:5)],TriGroupe=SummPart[,TriGroupe])\n+SummPartTron=merge(SummPartshort,ActMoyT,by.x="Code",by.y="IdExtrap")\n+SummPartTron=SummPartTron[order(TriGroupe,decreasing=T),]\n+\n+ListSession=levels(as.factor(IdC2M$Session))\n+brks <- quantile(ActMoyTA$x, probs = seq(.05, .95, .05), na.rm = TRUE)-1\n+clrs <- round(seq(255, 40, length.out = length(brks) + 1), 0) %>%\n+{paste0("rgb(255,", ., ",", ., ")")}\n+\n+\n+#to do: extend colors to other columns to improve readability\n+SummHTMLT=datatable(SummPartTron, rownames = FALSE) %>%\n+ formatStyle(columns = c("Code","Groupe","Nom francais","Nom scientifique","Risque d\'erreur (%)"),valueColumns="Risque d\'erreur (%)", \n+ background = styleInterval(c(1, 10, 50), c("white", "khaki", "orange", "orangered"))) %>%\n+ formatStyle(columns=ListSession, backgroundColor = styleInterval(brks, clrs))\n+\n+saveWidget(SummHTMLT,"output-detailRP.html")\n+write.table(SummPartTron,"output-detailRP.tabular",row.names=F,sep="\\t",quote=FALSE)\n' |
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| diff -r 000000000000 -r c55e09a8b4c8 BilanEnrichiRPen.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BilanEnrichiRPen.xml Wed Mar 13 11:17:44 2019 -0400 |
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| @@ -0,0 +1,56 @@ +<tool id="vigiechiro_bilanenrichirp" name="Advanced restitution: 'Routier'or 'Pedestre' protocols" version="@VERSION@"> + <description>from Animal Detection on Acoustic Recordings</description> + <macros> + <import>vigiechiro_macros.xml</import> + </macros> + <expand macro="vigiechiro_bilanPF_bilanRP_requirements"/> + <command detect_errors="exit_code"><![CDATA[ + Rscript '$__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> |
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| diff -r 000000000000 -r c55e09a8b4c8 SpeciesList.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SpeciesList.csv Wed Mar 13 11:17:44 2019 -0400 |
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| b"@@ -0,0 +1,214 @@\n+Esp;Nesp;France;Turquie;Espagne;Norfolk;Scientific name;Group;NomFR;GroupFR\n+Aegcau;piaf;x;x;x;x;Aegithalos caudatus;bird;M\xe9sange \xe0 longue queue;Autre\n+Alcatt;piaf;x;x;x;x;Alcedo atthis;bird;Martin-p\xeacheur d'Europe;Autre\n+amph;amph;x;x;x;x;Amphibia sp.;frog;Amphibien sp.;Autre\n+Antius;Antius;x;;x;;Antaxius spinibrachius;bush-cricket;Antaxie voyageuse;Sauterelle\n+Antped;Antped;x;;;;Antaxius pedestris;bush-cricket;Antaxie marbree;Sauterelle\n+Antpet;piaf;x;x;;;Anthus petrosus;bird;Pipit maritime;Autre\n+Antsor;Antsor;x;;;;Antaxius sorrezensis;bush-cricket;Antaxie cevenole;Sauterelle\n+Apoagr;Aposp;x;;;;Apodemus agrarius;other mammal;Mulot ray\xe9;Autre\n+Apofla;Aposp;x;x;x;;Apodemus flavicollis;other mammal;Mulot \xe0 collier;Autre\n+Aposp;Aposp;x;x;x;x;Apodemus sp.;other mammal;Mulot sp.;Autre\n+Aposyl;Aposp;x;x;x;x;Apodemus sylvaticus;other mammal;Mulot sylvestre;Autre\n+Apuapu;piaf;x;x;x;x;Apus apus;bird;Martinet noir;Autre\n+Barbar;Barbar;x;x;x;x;Barbastella barbastellus;bat;Barbastelle d'Europe;Chauve-souris\n+Barfis;Barfis;x;;;;Barbitistes fischeri;bush-cricket;Barbitiste languedocien;Sauterelle\n+Barsan;Barsan;x;;x;;Barbitistes 'sanzii';bush-cricket;Barbitiste cryptique;Sauterelle\n+Barser;Barser;x;;x;;Barbitistes serricauda;bush-cricket;Barbitiste des bois;Sauterelle\n+Bicbic;Bicbic;x;;x;;Bicolorana bicolor;bush-cricket;Decticelle bicolore;Sauterelle\n+buzz;noise;x;x;x;x;insect wingbeats;noise;bourdonnement;Autre\n+car;noise;x;x;x;x;vehicle;noise;v\xe9hicule;Autre\n+Carcar;piaf;x;x;x;x;Carduelis carduelis;bird;Chardonneret \xe9l\xe9gant;Autre\n+Cerbra;piaf;x;x;x;x;Certhia brachydactyla;bird;Grimpereau des jardins;Autre\n+Cetcet;piaf;x;x;x;x;Cettia cettia;bird;Bouscarle de Cetti;Autre\n+chirp;chirp;x;;;;chirp;noise;chirp;Autre\n+Chlchl;piaf;x;x;x;x;Chloris chloris;bird;Verdier d'Europe;Autre\n+Chovag;criq;x;x;x;x;Chorthippus vagans;grasshopper;Criquet des pins;Autre\n+Cicatr;Cicatr;x;x;x;;Cicadatra atra;cicada;Cigale noire;Autre\n+Cicorn;Cicorn;x;x;x;;Cicada orni;cicada;Cigale grise;Autre\n+Cisjun;piaf;x;x;x;x;Cisticola juncidis;bird;Cisticole des joncs;Autre\n+Concon;Concon;x;x;x;;Conocephalus conocephalus;bush-cricket;Conoc\xe9phale africain;Sauterelle\n+Condor;Condor;x;x;x;x;Conocephalus dorsalis;bush-cricket;Conocephale des marais;Sauterelle\n+Confus;Confus;x;;x;x;Conocephalus fuscus;bush-cricket;Conocephale bigarre;Sauterelle\n+Corcho;Epheph;x;;;;Corsteropleurus chopardi;bush-cricket;Ephippig\xe8re corse;Sauterelle\n+Cornix;piaf;x;x;x;x;Corvus cornix;bird;Corneille mantel\xe9e;Autre\n+criq;criq;x;x;x;x;Caelifera sp.;grasshopper;Criquet sp.;Autre\n+Crorus;Mussp;x;x;x;x;Crocidura russula;other mammal;Crocidure musette;Autre\n+Cyacae;piaf;x;x;x;x;Cyanistes caerulea;bird;M\xe9sange bleue;Autre\n+Cympud;Cympud;x;;x;;Cymbalophora pudica;moth;Ecaille pudique;Autre\n+Cyrscu;Cyrscu;x;;x;;Cyrtaspis scutatus;bush-cricket;Meconeme a bouclier;Sauterelle\n+Decalb;Decalb;x;x;x;;Decticus albifrons;bush-cricket;Dectique a front blanc;Sauterelle\n+Denmaj;piaf;x;x;x;x;Dendrocopos major;bird;Pic \xe9peiche;Autre\n+elec;noise;x;x;x;x;electronical noise;noise;parasite;Autre\n+Embcae;piaf;x;x;x;x;Emberiza caesia;bird;Bruant cendrillard;Autre\n+Embcal;piaf;x;x;x;x;Emberiza calandra;bird;Bruant proyer;Autre\n+Embcir;piaf;x;x;x;x;Emberiza cirlus;bird;Bruant zizi;Autre\n+Embcit;piaf;x;x;x;x;Emberiza citrinella;bird;Bruant jaune;Autre\n+Epheph;Epheph;x;;x;;Ephippiger ephippiger;bush-cricket;Ephippigere des vignes;Sauterelle\n+Eptana;Eptnil;x;x;;;Eptesicus anatolicus;bat;Serotine d'Anatolie;Chauve-souris\n+Eptisa;Eptisa;;;x;;Eptesicus isabellinus;bat;Serotine isabelle;Chauve-souris\n+Eptnil;Eptnil;x;;x;;Eptesicus nilssonii;bat;S\xe9rotine bor\xe9ale;Chauve-souris\n+Eptser;Eptser;x;x;x;x;Eptesicus serotinus;bat;Serotine commune;Chauve-souris\n+Erirub;piaf;x;x;x;x;Erithacus rubecula;bird;Rougegorge familier;Autre\n+Euccho;criq;x;x;x;x;Euchorthippus chopardii;grasshopper;Criquet des bragalous;Autre\n+Eumbor;gril;x;x;x;;Eumodycogryllus bordigalensis;ground-cricket;Grillon bordelais;Autre\n+Eupcha;Eupsp;x;x;;;Euph"..b"auve-souris\n+Rhifer;Rhifer;x;x;x;x;Rhinolophus ferrumequinum;bat;Grand Rhinolophe;Chauve-souris\n+Rhihip;Rhihip;x;x;x;x;Rhinolophus hipposideros;bat;Petit Rhinolophe;Chauve-souris\n+Rhimeh;Rhimeh;;x;x;;Rhinolophus mehelyi;bat;Rinolophe de Mehely;Chauve-souris\n+river;noise;x;x;x;x;watercourse;noise;cours d'eau;Autre\n+RodTu1;mamm;x;x;x;;Rodentia sp. from Turkey 1;other mammal;Rongeur de Turquie type 1;Autre\n+Roeroe;Roeroe;x;x;x;x;Roeseliana roeselii;bush-cricket;Decticelle bariolee;Sauterelle\n+Rusnit;Rusnit;x;x;x;x;Ruspolia nitidula;bush-cricket;Conocephale gracieux;Sauterelle\n+SauIn1;SauIn1;;;;;Tettigoniidae sp. from India 1;bush-cricket;Sauterelle sp. In1;Sauterelle\n+SauIn2;SauIn2;;;;;Tettigoniidae sp. from India 2;bush-cricket;Sauterelle sp. In2;Sauterelle\n+SauIn3;SauIn3;;;;;Tettigoniidae sp. from India 3;bush-cricket;Sauterelle sp. In3;Sauterelle\n+SauTu4;SauTu4;;x;;;Tettigoniidae sp. from Turkey 4;bush-cricket;Sauterelle sp. Tu4;Sauterelle\n+SauTu5;SauTu5;;x;;;Tettigoniidae sp. from Turkey 5;bush-cricket;Sauterelle sp. Tu5;Sauterelle\n+SauTu6;SauTu6;;x;;;Tettigoniidae sp. from Turkey 6;bush-cricket;Sauterelle sp. Tu6;Sauterelle\n+SauTu7;SauTu7;;x;;;Tettigoniidae sp. from Turkey 7;bush-cricket;Sauterelle sp. Tu7;Sauterelle\n+SauTurquiesp1;SauTurquiesp1;;x;;;Tettigoniidae sp. from Turkey 1;bush-cricket;Sauterelle sp. Tu1;Sauterelle\n+SauTurquiesp2;SauTurquiesp2;;x;;;Tettigoniidae sp. from Turkey 2;bush-cricket;Sauterelle sp. Tu2;Sauterelle\n+SauTurquiesp3;SauTurquiesp3;;x;;;Tettigoniidae sp. from Turkey 3;bush-cricket;Sauterelle sp. Tu3;Sauterelle\n+Sepsep;Sepsep;x;;x;;Sepiana sepium;bush-cricket;Decticelle echassiere;Sauterelle\n+Serser;piaf;x;x;x;x;Serinus serinus;bird;Serin cini;Autre\n+Siteur;piaf;x;x;x;x;Sitta europaea;bird;Sittelle torchepot;Autre\n+Sorcor;Mussp;x;x;x;x;Soricinus coronatus;bush-cricket;Musaraigne couronn\xe9e;Autre\n+Stralu;piaf;x;x;x;x;Strix aluco;bird;Effraie des clochers;Autre\n+Strdec;piaf;x;x;x;;Streptopelia decaocto;bird;Tourterelle turque;Autre\n+Stuvul;piaf;x;x;x;x;Sturnus vulgaris;bird;Etourneau sansonnet;Autre\n+Sylatr;piaf;x;x;x;x;Sylvia atricapilla;bird;Fauvette \xe0 t\xeate noire;Autre\n+Sylcom;piaf;x;x;x;x;Sylvia communis;bird;Fauvette grisette;Autre\n+Sylmel;piaf;x;x;x;x;Sylvia melanocephala;bird;Fauvette m\xe9lanoc\xe9phale;Autre\n+Tadten;Tadten;x;x;x;;Tadarida teniotis;bat;Molosse;Chauve-souris\n+Tesori;Tesori;;;;;Tessellana orina;bush-cricket;Decticelle orina;Sauterelle\n+Testes;Testes;x;x;x;;Tessellana tessellata;bush-cricket;Decticelle carroyee;Sauterelle\n+Tetarg;Tetarg;x;;x;;Tettigetta argentata;cicada;Cigale argentee;Autre\n+Tetcan;Tetcan;x;x;x;;Tettigonia cantans;bush-cricket;Sauterelle cymbaliere;Sauterelle\n+Tethis;Tethis;;;x;;Tettigonia hispanica;bush-cricket;Sauterelle hispanique;Sauterelle\n+Tetpyg;Tetpyg;x;;x;;Tettigetta pygmea;cicada;Cigale pygmee;Autre\n+Tetvir;Tetvir;x;x;x;x;Tettigonia viridissima;bush-cricket;Sauterelle verte;Sauterelle\n+Thycor;Thycor;x;;x;;Thyreonotus corsicus;bush-cricket;Decticelle marocaine;Sauterelle\n+Trotro;piaf;x;x;x;x;Troglodytes troglodytes;bird;Troglodyte mignon;Autre\n+Turmer;piaf;x;x;x;x;Turdus merula;bird;Merle noir;Autre\n+Turphi;piaf;x;x;x;x;Turdus philomelos;bird;Grive musicienne;Autre\n+Tyllil;Tyllil;x;x;x;;Tylopsis lilifolia;bush-cricket;Phaneroptere liliace;Sauterelle\n+Urobre;Urosp;x;;;;Uromenus brevicollis;bush-cricket;Ephippig\xe8re d'Alg\xe9rie;Sauterelle\n+Urorug;Urosp;x;;x;;Uromenus rugosicollis;bush-cricket;Ephippigere carenee;Sauterelle\n+Urosp;Urosp;x;x;;;Uromenus sp.;bush-cricket;Ephippig\xe8re car\xe9n\xe9e/d'Alg\xe9rie;Sauterelle\n+Vesmur;Vesmur;x;x;x;;Vespertilio murinus;bat;Serotine bicolore;Chauve-souris\n+wind;noise;x;x;x;x;wind;noise;vent;Autre\n+Yerbey;Yerbey;x;;;;Yersinella beybienkoi;bush-cricket;Decticelle italienne;Sauterelle\n+Yerbey;Yerbey;x;;;;Yersinella beybienkoi;bush-cricket;Decticelle italienne;Sauterelle\n+Yerray;Yerray;x;;x;;Yersinella raymondii;bush-cricket;Decticelle frele;Sauterelle\n+Zeuabb;Zeuabb;x;;x;;Zeuneriana abbreviata;bush-cricket;Decticelle aquitaine;Sauterelle\n" |
| b |
| diff -r 000000000000 -r c55e09a8b4c8 refRPSeuil50.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/refRPSeuil50.csv Wed Mar 13 11:17:44 2019 -0400 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r c55e09a8b4c8 test-data/BilanEnrichiRP_Test1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/BilanEnrichiRP_Test1.tabular Wed Mar 13 11:17:44 2019 -0400 |
| b |
| b'@@ -0,0 +1,1376 @@\n+nom du 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|
| b |
| diff -r 000000000000 -r c55e09a8b4c8 test-data/BilanEnrichiRP_Test1_out_tab.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/BilanEnrichiRP_Test1_out_tab.tabular Wed Mar 13 11:17:44 2019 -0400 |
| b |
| @@ -0,0 +1,5 @@ +Code Groupe Nom francais Nom scientifique Risque d'erreur (%) TriGroupe Canal 1 2 3 4 5 6 7 8 9 10 +Pippip Chauve-souris Pipistrelle commune Pipistrellus pipistrellus 77 3 Expansion 0 0 0 0 0 0 0 3 0 0 +Tetvir Sauterelle Sauterelle verte Tettigonia viridissima 10 2 Direct 0 0 1 0 1 0 0 1 3 0 +noise Autre bruit noise 1 1 Direct 58 20 73 74 72 73 72 62 69 74 +noise Autre bruit noise 1 1 Expansion 58 72 74 78 73 72 73 73 72 74 |
| b |
| diff -r 000000000000 -r c55e09a8b4c8 vigiechiro_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vigiechiro_macros.xml Wed Mar 13 11:17:44 2019 -0400 |
| b |
| @@ -0,0 +1,40 @@ +<macros> + <token name="@VERSION@">0.1.0</token> + <xml name="vigiechiro_bibref"> + <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> + </xml> + <xml name="vigiechiro_bilanPF_bilanRP_requirements"> + <requirements> + <requirement type="package" version="1.4.3">r-reshape2</requirement> + <requirement type="package" version="1.11.4">r-data.table</requirement> + <requirement type="package" version="0.4">r-dt</requirement> + <requirement type="package" version="1.2">r-htmlwidgets</requirement> + <requirement type="package" version="2.6">pandoc</requirement> + </requirements> + </xml> +</macros> |