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Commit message:
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271 |
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modified:
BilanEnrichiRP.R BilanEnrichiRPen.xml SpeciesList.csv test-data/BilanEnrichiRP_Test1.tabular test-data/BilanEnrichiRP_Test1_out_tab.tabular vigiechiro_macros.xml |
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| diff -r c55e09a8b4c8 -r be4e28da3919 BilanEnrichiRP.R --- a/BilanEnrichiRP.R Wed Mar 13 11:17:44 2019 -0400 +++ b/BilanEnrichiRP.R Fri Apr 26 12:17:22 2019 -0400 |
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| b'@@ -1,184 +1,192 @@\n+#!/usr/bin/env Rscript\n+\n+args <- commandArgs(trailingOnly = TRUE)\n+\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+EchelleErreur=c("","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+IdC2=fread(args[1],encoding="UTF-8")\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+# print("Protocole non conforme, ce script doit etre lance uniquement pour un protocole Routier ou Pedestre")\n+ print("Wrong protocol, please only use this tool for a \\\'Pedestre\\\' or \\\'Routier\\\' protocol.")\n+}els'..b'(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+ #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@@ -189,32 +197,35 @@\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+ saveWidget(SummHTML,"output-summaryRP.html")\n+ write.table(SummPart,"output-summaryRP.tabular",row.names=F,sep="\\t")\n+ #write.csv2(SummPart,"output-summaryRP.tabular",row.names=F) #for testing\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+ saveWidget(SummHTMLT,"output-detailRP.html")\n+ write.table(SummPartTron,"output-detailRP.tabular",row.names=F,sep="\\t")\n+# write.csv2(SummPartTron,"output-detailRP.tabular",row.names=F)#for testing\n+}\n' |
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| diff -r c55e09a8b4c8 -r be4e28da3919 BilanEnrichiRPen.xml --- a/BilanEnrichiRPen.xml Wed Mar 13 11:17:44 2019 -0400 +++ b/BilanEnrichiRPen.xml Fri Apr 26 12:17:22 2019 -0400 |
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| @@ -2,8 +2,10 @@ <description>from Animal Detection on Acoustic Recordings</description> <macros> <import>vigiechiro_macros.xml</import> - </macros> - <expand macro="vigiechiro_bilanPF_bilanRP_requirements"/> + </macros> + <expand macro="vigiechiro_requirements"> + <expand macro="vigiechiro_bilanenrichi_requirements"/> + </expand> <command detect_errors="exit_code"><![CDATA[ Rscript '$__tool_directory__/BilanEnrichiRP.R' '$idc2' |
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| diff -r c55e09a8b4c8 -r be4e28da3919 SpeciesList.csv --- a/SpeciesList.csv Wed Mar 13 11:17:44 2019 -0400 +++ b/SpeciesList.csv Fri Apr 26 12:17:22 2019 -0400 |
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| b"@@ -1,214 +1,390 @@\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;;;Eu"..b"ubetra;bird;Tarier des pr\xe9s;Autre\n+Saxrubi;piaf;piaf;x;;;x;Saxicola rubicola;bird;Tarier p\xe2tre;Autre\n+Scorus;piaf;piaf;x;;;x;Scolopax rusticola;bird;B\xe9casse des bois;Autre\n+Sepsep;Sepsep;Sepsep;x;;x;;Sepiana sepium;bush-cricket;Decticelle echassiere;Sauterelle\n+Serser;piaf;piaf;x;x;x;x;Serinus serinus;bird;Serin cini;Autre\n+Siteur;piaf;piaf;x;x;x;x;Sitta europaea;bird;Sittelle torchepot;Autre\n+Sorcor;Mussp;Mussp;x;x;x;x;Soricinus coronatus;other mammal;Musaraigne couronn\xe9e;Autre\n+Spispi;piaf;piaf;x;;;x;Spinus spinus;bird;Tarin des aulnes;Autre\n+Stralu;piaf;piaf;x;x;x;x;Strix aluco;bird;Chouette hulotte;Autre\n+Strdec;piaf;piaf;x;x;x;;Streptopelia decaocto;bird;Tourterelle turque;Autre\n+Stuvul;piaf;piaf;x;x;x;x;Sturnus vulgaris;bird;Etourneau sansonnet;Autre\n+Susscr;Susscr;Susscr;x;;;;Sus scrofa;other mammal;Sanglier;Autre\n+Sylatr;piaf;piaf;x;x;x;x;Sylvia atricapilla;bird;Fauvette \xe0 t\xeate noire;Autre\n+Sylbor;piaf;piaf;x;;;x;Sylvia borin;bird;Fauvette des jardins;Autre\n+Sylcan;piaf;piaf;x;;;;Sylvia cantillans;bird;Fauvette passerinette;Autre\n+Sylcom;piaf;piaf;x;x;x;x;Sylvia communis;bird;Fauvette grisette;Autre\n+Sylcur;piaf;piaf;x;;;x;Sylvia curruca;bird;Fauvette babillarde;Autre\n+Sylmel;piaf;piaf;x;x;x;x;Sylvia melanocephala;bird;Fauvette m\xe9lanoc\xe9phale;Autre\n+Sylund;piaf;piaf;x;;;x;Sylvia undata;bird;Fauvette pitchou;Autre\n+Tadten;Tadten;Tadten;x;x;x;;Tadarida teniotis;bat;Molosse;Chauve-souris\n+Tamsib;Tamsib;Tamsib;x;;;;Tamias sibiricus;other mammal;Tamia de Sib\xe9rie;Autre\n+Tesori;Tesori;Tesori;;;;;Tessellana orina;bush-cricket;Decticelle orina;Sauterelle\n+Testes;Testes;Testes;x;x;x;;Tessellana tessellata;bush-cricket;Decticelle carroyee;Sauterelle\n+Tetarg;Tetarg;Tetarg;x;;x;;Tettigetta argentata;cicada;Cigale argentee;Autre\n+Tetcan;Tetcan;Tetvir;x;x;x;;Tettigonia cantans;bush-cricket;Sauterelle cymbaliere;Sauterelle\n+Tethis;Tethis;Tetvir;;;x;;Tettigonia hispanica;bush-cricket;Sauterelle hispanique;Sauterelle\n+Tetpyg;Tetpyg;Tetpyg;x;;x;;Tettigetta pygmea;cicada;Cigale pygmee;Autre\n+Tetvir;Tetvir;Tetvir;x;x;x;x;Tettigonia viridissima;bush-cricket;Sauterelle verte;Sauterelle\n+Thycor;Thycor;Thycor;x;;x;;Thyreonotus corsicus;bush-cricket;Decticelle marocaine;Sauterelle\n+Trineb;piaf;piaf;x;;;x;Tringa nebularia;bird;Chevalier aboyeur;Autre\n+Trioch;piaf;piaf;x;;;x;Tringa ochropus;bird;Chevalier culblanc;Autre\n+Tritot;piaf;piaf;x;;;x;Tringa totanus;bird;Chevalier gambette;Autre\n+Trotro;piaf;piaf;x;x;x;x;Troglodytes troglodytes;bird;Troglodyte mignon;Autre\n+Turili;piaf;piaf;x;;;x;Turdus iliacus;bird;Grive mauvis;Autre\n+Turmer;piaf;piaf;x;x;x;x;Turdus merula;bird;Merle noir;Autre\n+Turphi;piaf;piaf;x;x;x;x;Turdus philomelos;bird;Grive musicienne;Autre\n+Turpil;piaf;piaf;x;x;x;x;Turdus pilaris;bird;Grive litorne;Autre\n+Turvis;piaf;piaf;x;;;x;Turdus viscivorus;bird;Grive draine;Autre\n+Tyllil;Tyllil;Tyllil;x;x;x;;Tylopsis lilifolia;bush-cricket;Phaneroptere liliace;Sauterelle\n+Tytalb;piaf;piaf;x;;;x;Tyto alba;bird;Effraie des clochers;Autre\n+Urobre;Urosp;Urosp;x;;;;Uromenus brevicollis;bush-cricket;Ephippig\xe8re d'Alg\xe9rie;Sauterelle\n+Urorug;Urosp;Urosp;x;;x;;Uromenus rugosicollis;bush-cricket;Ephippigere carenee;Sauterelle\n+Urosp;Urosp;Urosp;x;x;;;Uromenus sp.;bush-cricket;Ephippig\xe8re car\xe9n\xe9e/d'Alg\xe9rie;Sauterelle\n+Vanvan;piaf;piaf;x;;;x;Vanellus vanellus;bird;Vanneau hupp\xe9;Autre\n+Vesmur;Vesmur;Vesmur;x;x;x;;Vespertilio murinus;bat;Serotine bicolore;Chauve-souris\n+Vulvul;Vulvul;Vulvul;x;;;x;Vulpes vulpes;other mammal;Renard roux;Autre\n+wind;noise;noise;x;x;x;x;wind;noise;vent;Autre\n+wings;wings;wings;x;;;x;wings;noise;battements;Autre\n+Xencin;piaf;piaf;x;x;x;x;Xenus cinereus;bird;Chevalier bargette;Autre\n+Yerbey;Yerbey;Yerbey;x;;;;Yersinella beybienkoi;bush-cricket;Decticelle italienne;Sauterelle\n+Yerray;Yerray;Yerray;x;;x;;Yersinella raymondii;bush-cricket;Decticelle frele;Sauterelle\n+Yposp;Yposp;Yposp;x;x;x;x;Yponomeuta sp.;moth;Hyponomeute sp.;Autre\n+Zeuabb;Metbra;Metbra;x;;x;;Zeuneriana abbreviata;bush-cricket;Decticelle aquitaine;Sauterelle\n" |
| b |
| diff -r c55e09a8b4c8 -r be4e28da3919 test-data/BilanEnrichiRP_Test1.tabular --- a/test-data/BilanEnrichiRP_Test1.tabular Wed Mar 13 11:17:44 2019 -0400 +++ b/test-data/BilanEnrichiRP_Test1.tabular Fri Apr 26 12:17:22 2019 -0400 |
| b |
| b'@@ -1,1376 +1,1837 @@\n-nom du 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|
| b |
| diff -r c55e09a8b4c8 -r be4e28da3919 test-data/BilanEnrichiRP_Test1_out_tab.tabular --- a/test-data/BilanEnrichiRP_Test1_out_tab.tabular Wed Mar 13 11:17:44 2019 -0400 +++ b/test-data/BilanEnrichiRP_Test1_out_tab.tabular Fri Apr 26 12:17:22 2019 -0400 |
| b |
| @@ -1,5 +1,44 @@ -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 +"Code" "Groupe" "Nom francais" "Nom scientifique" "Risque d'erreur (%)" "TriGroupe" "Canal" "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" +"Eptser" "Chauve-souris" "Serotine commune" "Eptesicus serotinus" "97" 3 "Direct" 0 0 0 0 0 0 0 1 0 1 +"Myoema" "Chauve-souris" "Murin a oreilles echancrees" "Myotis emarginatus" "95" 3 "Expansion" 0 0 0 0 1 0 1 0 0 0 +"Nyclei" "Chauve-souris" "Noctule de Leisler" "Nyctalus leisleri" "1" 3 "Direct" 6 4 1 2 1 7 1 4 0 1 +"Nycnoc" "Chauve-souris" "Noctule commune" "Nyctalus noctula" "15" 3 "Direct" 0 6 0 1 0 3 0 5 0 1 +"Pipkuh" "Chauve-souris" "Pipistrelle de Kuhl" "Pipistrellus kuhlii" "92" 3 "Direct" 0 0 0 0 0 0 0 1 3 0 +"Pipkuh" "Chauve-souris" "Pipistrelle de Kuhl" "Pipistrellus kuhlii" "92" 3 "Expansion" 0 0 1 0 0 0 0 2 0 1 +"Pipnat" "Chauve-souris" "Pipistrelle de Nathusius" "Pipistrellus nathusii" "53" 3 "Direct" 0 1 1 0 0 0 0 1 0 1 +"Pippip" "Chauve-souris" "Pipistrelle commune" "Pipistrellus pipistrellus" "1" 3 "Direct" 0 10 1 23 35 11 5 17 1 0 +"Pippip" "Chauve-souris" "Pipistrelle commune" "Pipistrellus pipistrellus" "1" 3 "Expansion" 6 6 3 2 6 12 2 2 1 3 +"Pippyg" "Chauve-souris" "Pipistrelle soprane" "Pipistrellus pygmaeus" "95" 3 "Expansion" 0 0 1 0 0 0 0 0 0 0 +"Rhieur" "Chauve-souris" "Rhinolophe euryale" "Rhinolophus euryale" "75" 3 "Expansion" 0 1 0 0 0 1 0 0 0 0 +"Rhifer" "Chauve-souris" "Grand Rhinolophe" "Rhinolophus ferrumequinum" "97" 3 "Expansion" 0 0 0 0 0 1 0 0 0 0 +"Rhihip" "Chauve-souris" "Petit Rhinolophe" "Rhinolophus hipposideros" "6" 3 "Expansion" 0 0 0 0 1 1 1 0 0 0 +"Barfis" "Sauterelle" "Barbitiste languedocien" "Barbitistes fischeri" "59" 2 "Expansion" 0 0 0 1 0 0 0 0 0 0 +"Confus" "Sauterelle" "Conocephale bigarre" "Conocephalus fuscus" "97" 2 "Expansion" 0 0 0 0 0 1 0 0 0 0 +"Epheph" "Sauterelle" "Ephippigere des vignes" "Ephippiger ephippiger" "10" 2 "Direct" 0 1 0 6 3 0 0 0 0 0 +"Epheph" "Sauterelle" "Ephippigere des vignes" "Ephippiger ephippiger" "10" 2 "Expansion" 0 0 0 0 0 0 0 1 0 0 +"Isopyr" "Sauterelle" "Barbatiste pyreneen" "Isophya pyrenaea" "2" 2 "Direct" 0 0 1 5 1 0 0 1 0 0 +"Isopyr" "Sauterelle" "Barbatiste pyreneen" "Isophya pyrenaea" "2" 2 "Expansion" 0 0 0 3 0 2 0 3 0 1 +"Leppun" "Sauterelle" "Sauterelle ponctuee" "Leptophyes punctatissima" "39" 2 "Direct" 1 1 4 3 1 3 1 1 0 0 +"Phafal" "Sauterelle" "Phaneroptere commun" "Phaneroptera falcata" "91" 2 "Direct" 0 0 0 2 0 0 0 0 0 0 +"Phanan" "Sauterelle" "Phaneroptere meridional" "Phaneroptera nana" "77" 2 "Direct" 0 2 2 0 1 0 0 0 0 0 +"Phanan" "Sauterelle" "Phaneroptere meridional" "Phaneroptera nana" "77" 2 "Expansion" 0 0 0 2 0 0 0 0 0 0 +"Phogri" "Sauterelle" "Decticelle cendree" "Pholidoptera griseoaptera" "4" 2 "Direct" 4 8 7 17 7 8 2 12 0 4 +"Phogri" "Sauterelle" "Decticelle cendree" "Pholidoptera griseoaptera" "4" 2 "Expansion" 0 0 1 1 0 2 0 0 1 0 +"Plaalb" "Sauterelle" "Decticelle chagrinee" "Platycleis albopunctata" "95" 2 "Direct" 0 0 0 2 0 0 0 0 0 0 +"Plaint" "Sauterelle" "Decticelle intermediaire" "Platycleis intermedia" "92" 2 "Direct" 0 1 1 1 0 0 0 1 0 0 +"Plaint" "Sauterelle" "Decticelle intermediaire" "Platycleis intermedia" "92" 2 "Expansion" 0 0 1 0 0 0 0 1 0 0 +"Roeroe" "Sauterelle" "Decticelle bariolee" "Roeseliana roeselii" "72" 2 "Direct" 0 0 0 0 0 0 0 0 0 1 +"Roeroe" "Sauterelle" "Decticelle bariolee" "Roeseliana roeselii" "72" 2 "Expansion" 0 0 0 0 0 1 0 1 0 0 +"Rusnit" "Sauterelle" "Conocephale gracieux" "Ruspolia nitidula" "94" 2 "Direct" 0 0 0 0 0 3 0 0 0 0 +"Rusnit" "Sauterelle" "Conocephale gracieux" "Ruspolia nitidula" "94" 2 "Expansion" 0 0 0 1 0 0 0 0 0 0 +"Sepsep" "Sauterelle" "Decticelle echassiere" "Sepiana sepium" "96" 2 "Expansion" 0 0 0 0 0 0 0 1 0 0 +"Testes" "Sauterelle" "Decticelle carroyee" "Tessellana tessellata" "82" 2 "Direct" 2 1 0 5 0 0 1 0 0 2 +"Tetvir" "Sauterelle" "Sauterelle verte" "Tettigonia viridissima" "22" 2 "Direct" 2 10 6 11 8 7 5 4 3 21 +"Tetvir" "Sauterelle" "Sauterelle verte" "Tettigonia viridissima" "22" 2 "Expansion" 3 4 3 13 2 7 0 17 0 3 +"Urosp" "Sauterelle" "Ephippigère carénée/d'Algérie" "Uromenus sp." "90" 2 "Direct" 0 0 0 1 1 0 1 1 0 0 +"Urosp" "Sauterelle" "Ephippigère carénée/d'Algérie" "Uromenus sp." "90" 2 "Expansion" 0 0 0 3 0 1 0 0 0 0 +"Yerray" "Sauterelle" "Decticelle frele" "Yersinella raymondii" "99" 2 "Expansion" 0 0 0 0 0 1 0 0 0 0 +"Ratnor" "Autre" "Surmulot" "Rattus norvegicus" "93" 1 "Direct" 0 1 0 0 0 0 0 0 0 0 +"noise" "Autre" "bruit" "noise" "1" 1 "Direct" 73 74 73 72 70 72 72 72 72 73 +"noise" "Autre" "bruit" "noise" "1" 1 "Expansion" 67 61 64 71 63 72 35 73 26 68 +"piaf" "Autre" "Oiseau sp." "Aves sp." "4" 1 "Direct" 1 0 1 0 0 4 0 1 0 0 |
| b |
| diff -r c55e09a8b4c8 -r be4e28da3919 vigiechiro_macros.xml --- a/vigiechiro_macros.xml Wed Mar 13 11:17:44 2019 -0400 +++ b/vigiechiro_macros.xml Fri Apr 26 12:17:22 2019 -0400 |
| b |
| @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION@">0.1.0</token> + <token name="@VERSION@">0.1.1</token> <xml name="vigiechiro_bibref"> <citations> <citation type="bibtex"> @@ -28,13 +28,16 @@ <citation type="doi">10.5334/jors.154</citation> </citations> </xml> - <xml name="vigiechiro_bilanPF_bilanRP_requirements"> + <xml name="vigiechiro_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> + <requirement type="package" version="1.12.2">r-data.table</requirement> + <yield /> + </requirements> + </xml> + <xml name="vigiechiro_bilanenrichi_requirements"> + <requirement type="package" version="1.4.3">r-reshape2</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> </xml> </macros> |