| Next changeset 1:eb19a5089b56 (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:
IdValid.R IdValiden.xml Referentiel_seuils_C2.csv test-data/BilanEnrichiPF_Test1.tabular test-data/IdCor2Layer_Test1_out.tabular vigiechiro_macros.xml |
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| diff -r 000000000000 -r 8c472c4f1bf5 IdValid.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/IdValid.R Wed Mar 13 11:18:58 2019 -0400 |
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| @@ -0,0 +1,165 @@ +#!/usr/bin/env Rscript + +suppressMessages(library(data.table)) + +ValidHier=function(x,y) #used to write validator id over observer id +{ + #cat(y) + if(is.na(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) + + +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$validateur_probabilite) + + + +#Step 2: Get numerictime data +suppressWarnings(IdCorrect$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$ProbEsp_C2bs))[j]) + if(sum(is.na(IdSp$IdV))==(nrow(IdSp))) #case 1 : no validation no change + { + IdC2=rbind(IdC2,IdSp) + IdExtrap=c(IdExtrap,rep(IdSp$ProbEsp_C2bs[1],nrow(IdSp))) + TypeE=c(TypeE,rep(0,nrow(IdSp))) + }else{ #case 2: some validation + Vtemp=subset(IdSp,is.na(IdSp$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$`nom du fichier`),] +#discard duplicated species within the same files (= false positives corrected by 2nd layer) +IdC2=unique(IdC2,by=c("nom du fichier","IdExtrap")) + +write.table(IdC2,"output.tabular",row.names=F,sep="\t",quote=FALSE,na="NA") |
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| diff -r 000000000000 -r 8c472c4f1bf5 IdValiden.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/IdValiden.xml Wed Mar 13 11:18:58 2019 -0400 |
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| @@ -0,0 +1,46 @@ +<tool id="vigiechiro_idvalid" name="Tadarida identifications integration" version="@VERSION@"> + <description>Integrate identifications from animal detection on acoustic recordings</description> + <macros> + <import>vigiechiro_macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="1.10.4">r-data.table</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + Rscript '$__tool_directory__/IdValid.R' + '$inputfile' + '$__tool_directory__/Referentiel_seuils_C2.csv' + '$output' +]]> + </command> + <inputs> + <param name="inputfile" type="data" format="tabular" label="Corrected observation file" help="Use output file from Tadarida data clean : a sampling session file corrected."/> + </inputs> + <outputs> + <data name="output" format="tabular" from_work_dir="output.tabular" label="${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 Tadarida data cleaner. +- The output is a single tabular file with validated Ids + ]]></help> + <expand macro="vigiechiro_bibref" /> +</tool> |
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| diff -r 000000000000 -r 8c472c4f1bf5 Referentiel_seuils_C2.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Referentiel_seuils_C2.csv Wed Mar 13 11:18:58 2019 -0400 |
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| b'@@ -0,0 +1,77 @@\n+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\n+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\n+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\n+Rhihip;-5.969614204;11.40700358;0.524;0.716;0.225;0.35;0.099585062;0.056994819;-5.819466659;11.41414973;0.51;0.703;0.221428571;0.321428571;0.084033613;0.054726368;0.18289497;0.170404281;0.931705672;0.933067009;0.182628128;Rhihip;0.225;0.353571429;0.099585062;0.052356021;-5.790678559;11.13511299;0.521;0.718\n+Barbar;-5.673386605;11.75110344;0.483;0.67;0.291366906;0.356115108;0.08372093;0.057894737;-5.564489618;11.74868047;0.474;0.661;0.321285141;0.389558233;0.10106383;0.067484663;0.19727442;0.219847966;1.114427132;1.033526108;0.212716413;Barbar;0.309236948;0.385542169;0.094736842;0.061349693;-5.561291853;11.24861482;0.495;0.69\n+Rusnit;-5.761885307;27.00734744;0.214;0.295;0.369491525;0.379661017;0.046153846;0.021390374;-5.999840427;37.36156155;0.161;0.22;0.397959184;0.413265306;0.070866142;0.025423729;0.204174191;0.22687859;1.111201123;1.001041207;0.226642608;Rusnit;0.408163265;0.408163265;0.056910569;0.033333333;-5.880405916;32.26404124;0.183;0.251\n+Myonat;-5.634559403;11.86614368;0.475;0.661;0.338645418;0.474103586;0.117021277;0.050359712;-5.528792174;11.69073573;0.473;0.661;0.331950207;0.443983402;0.095505618;0.042857143;0.245032498;0.228574093;0.932831744;0.962409212;0.237501979;Myonat;0.32780083;0.452282158;0.119565217;0.050359712;-5.527766673;11.52009507;0.48;0.671\n+Nyclei;-4.935905731;10.51420089;0.47;0.679;0.382882883;0.45045045;0.121794872;0.057915058;-4.867531773;10.39089138;0.469;0.68;0.36097561;0.443902439;0.105802048;0.053941909;0.253260816;0.241155501;0.952202182;1.011251568;0.238472314;Nyclei;0.36097561;0.429268293;0.114864865;0.048780488;-4.875184583;10.49761466;0.465;0.674\n+Nycnoc;-5.915598202;13.74409497;0.431;0.591;0.398963731;0.492227979;0.165467626;0.066666667;-6.139379694;17.74192449;0.347;0.47;0.37012987;0.396103896;0.118181818;0.051020408;0.280831501;0.233858998;0.832737772;0.959975533;0.243609332;Nycnoc;0.344155844;0.435064935;0.151260504;0.043956044;-6.179570269;14.61424023;0.423;0.574\n+Lamsp.;-7.244082473;21.93899668;0.331;0.431;0.351851852;0.518518519;0.125;0.103448276;-6.954350212;18.69608095;0.372;0.49;0.377358491;0.528301887;0.153846154;0.137931034;0.274704662;0.299359391;1.089749951;1.159077941;0.258273737;Lamsp.;0.339622642;0.471698113;0.125;0.096774194;-7.11431275;21.74802941;0.328;0.429\n+Leppun;-4.219470191;9.460363122;0.447;0.679;0.35551142;0.550148957;0.120596206;0.111764706;-4.315732499;9.578325998;0.451;0.68;0.295641932;0.551236749;0.123167155;0.120092379;0.284505322;0.272534554;0.957924272;1.017906068;0.267740376;Leppun;0.293286219;0.542991755;0.126637555;0.108045977;-4.368656949;9.338141008;0.468;0.704\n+Pippip;-3.700038171;8.471925149;0.437;0.697;0.318051576;0.58739255;0.14017341;0.119804401;-3.791687392;8.188349216;0.464;0.732;0.288392213;0.583273252;0.143972246;0.120243531;0.291355484;0.283970311;0.974652361;1.004162485;0.282793188;Pippip;0.281903389;0.584715213;0.147989735;0.116564417;-3.82796986;8.341092474;0.459;0.723\n+Pleaus;-5.939604546;11.86576121;0.501;0.686;0.351694915;0.555084746;0.172972973;0.110169492;-5.900088719;11.82314875;0.5;0.685;0.308035714;0.571428571;0.171122995;0.127272727;0.297480531;0.294465002;0.989863103;1.016773712;0.289607214;Pleaus;0.330357143;0.540178571;0.175824176;0.112068966;-5.885720467;11.67405029;0.'..b'0.424\n+Decalb;-6.26328128;41.46237641;0.152;0.205;0.918918919;0.972972973;0.666666667;0.666666667;-6.146747664;47.78079953;0.129;0.175;0.904109589;1;0.5;1;0.806306306;0.851027397;1.055464146;1.078247035;0.789269406;Decalb;0.917808219;0.97260274;0.666666667;0.6;-6.108989447;40.27878201;0.152;0.207\n+Eptnil;-7.09881739;39.42396532;0.181;0.236;0.96;1;0.666666667;NaN;-6.900807963;40.69349629;0.17;0.224;1;1;1;NaN;0.875555556;1;1.14213198;1.14213198;0.875555556;Eptnil;0.96;1;0.666666667;NaN;-6.923361423;38.13078002;0.182;0.24\n+Inssp7;-7.15594089;89.73266508;0.08;0.105;0.958333333;1;0.75;1;-6.810368524;64.66269367;0.106;0.14;1;1;1;1;0.927083333;1;1.078651685;1.107692308;0.902777778;Inssp7;0.958333333;1;0.75;NaN;-6.988297976;86.69935725;0.081;0.106\n+Phofem;-6.284700415;37.71118876;0.167;0.225;0.987804878;1;0.875;1;-6.057110807;32.87618686;0.185;0.252;1;1;1;1;0.96570122;1;1.035516969;1.063400576;0.940379404;Phofem;0.987804878;1;0.833333333;NaN;-6.117618555;36.21632879;0.169;0.23\n+amph;-6.613007553;29.60649332;0.224;0.298;1;1;NaN;NaN;-6.453524869;25.19228889;0.257;0.344;1;1;NaN;NaN;1;1;1;1;1;amph;1;1;NaN;NaN;-6.428283677;29.23542026;0.22;0.296\n+Antius;-7.209034432;44.45763374;0.163;0.212;1;1;NaN;NaN;-7.093154616;62.64559091;0.114;0.149;1;1;NaN;NaN;1;1;1;1;1;Antius;1;1;NaN;NaN;-7.030447669;42.62283057;0.165;0.217\n+Antped;-7.383650573;54.11490894;0.137;0.178;1;1;NaN;NaN;-7.366972966;95.90806245;0.077;0.1;1;1;NaN;NaN;1;1;1;1;1;Antped;1;1;NaN;NaN;-7.338949392;77.28965393;0.095;0.124\n+Barfis;-7.280210474;79.98729907;0.092;0.119;1;1;NaN;NaN;-7.119002646;79.79382786;0.09;0.117;1;1;NaN;NaN;1;1;1;1;1;Barfis;1;1;NaN;NaN;-7.164452894;77.53293265;0.093;0.121\n+Barser;-6.900683371;57.16826361;0.121;0.16;1;1;NaN;NaN;-6.747200288;67.29234702;0.101;0.133;1;1;NaN;NaN;1;1;1;1;1;Barser;1;1;NaN;NaN;-6.720980361;53.61251354;0.126;0.167\n+Bicbic;-7.003205608;-42.11519506;Inf;Inf;1;1;NaN;NaN;-6.840974246;-3251.15631;Inf;Inf;1;1;NaN;NaN;1;1;1;1;1;Bicbic;1;1;NaN;NaN;-6.88877136;-34.19678581;Inf;Inf\n+Concon;-7.03108139;9.716391437;0.724;0.95;1;1;NaN;NaN;-6.896771627;28.02818149;0.247;0.325;1;1;NaN;NaN;1;1;1;1;1;Concon;1;1;NaN;NaN;-6.837427338;0.725449539;Inf;Inf\n+Corcho;-6.078521756;46.46199314;0.131;0.179;1;1;NaN;NaN;-5.943690586;58.34822938;0.102;0.14;1;1;NaN;NaN;1;1;1;1;1;Corcho;1;1;NaN;NaN;-5.896190668;43.50768289;0.136;0.187\n+gril;-7.555488435;57.43438716;0.132;0.17;1;1;NaN;NaN;-7.314404425;53.32962265;0.138;0.179;1;1;NaN;NaN;1;1;1;1;1;gril;1;1;NaN;NaN;-7.374075354;55.22552599;0.134;0.174\n+Lyrple;-7.395620042;44.41474239;0.167;0.216;1;1;1;1;-7.224794267;31.41678532;0.23;0.3;1;1;1;1;1;1;1;1;1;Lyrple;1;1;1;1;-7.218299801;43.07791371;0.168;0.219\n+Metsau;-7.263224642;32.44449421;0.224;0.292;1;1;NaN;NaN;-7.167714665;52.63620533;0.137;0.178;1;1;NaN;NaN;1;1;1;1;1;Metsau;1;1;NaN;NaN;-7.077134949;26.37920707;0.269;0.352\n+Myobra;-7.352433699;50.75933419;0.145;0.189;1;1;NaN;NaN;-7.175938172;49.8921739;0.144;0.188;1;1;NaN;NaN;1;1;1;1;1;Myobra;1;1;NaN;NaN;-7.173365265;48.37787777;0.149;0.194\n+Phafal;-7.544411986;62.8376307;0.121;0.156;0.947368421;1;0.8;1;-7.721059773;59.19348597;0.131;0.168;1;1;1;1;0.936842105;1;1.06741573;1;1;Phafal;1;1;1;1;-7.751398334;62.73816799;0.124;0.159\n+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\n+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\n+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\n+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\n+Ratnor;-7.634127214;58.5655848;0.131;0.168;1;1;1;NaN;;;;;;;;;1;#DIV/0!;#DIV/0!;#DIV/0!;#DIV/0!;;;;;;;;;\n' |
| b |
| diff -r 000000000000 -r 8c472c4f1bf5 test-data/BilanEnrichiPF_Test1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/BilanEnrichiPF_Test1.tabular Wed Mar 13 11:18:58 2019 -0400 |
| b |
| b'@@ -0,0 +1,1119 @@\n+nom du fichier\ttadarida_taxon\ttemps_debut\ttemps_fin\tfrequence_mediane\ttadarida_probabilite\ttadarida_taxon_autre\tobservateur_taxon\tobservateur_probabilite\tvalidateur_taxon\tvalidateur_probabilite\tparticipation\tamph\tAntius\tAntped\tAntsor\tAposp\tBarbar\tBarfis\tBarsan\tBarser\tBicbic\tchirp\tCicatr\tCicorn\tConcon\tConfus\tCorcho\tcriq\tCympud\tCyrscu\tDecalb\tEpheph\tEptnil\tEptser\tEupsp\tgril\tHypsav\tInsp11\tInsp12\tInssp5\tInssp6\tInssp7\tInssp8\tInssp9\tIsopyr\tLamsp.\tLeppun\tLyrple\tmamm\tMetsau\tMicagr\tMinsch\tMussp\tMyoalc\tMyobec\tMyobra\tMyocap\tMyodas\tMyodau\tMyoema\tMyoGT\tMyomys\tMyonat\tnoise\tNyclas\tNyclei\tNycnoc\tOrtsp.\tPhafal\tPhanan\tPhofem\tPhogri\tpiaf\tPipkuh\tPipnat\tPippip\tPippyg\tPlaaff\tPlaalb\tPlafal\tPlaint\tPlasab\tPleaur\tPleaus\tPlemac\tPtebon\tPtecor\tPteger\tPtepon\tRatnor\tRhieur\tRhifer\tRhihip\tRoeroe\tRusnit\tSepsep\tTadten\tTestes\tTetcan\tTetpyg\tTetvir\tThycor\tTyllil\tUrobre\tUrorug\tVesmur\tYerbey\tYerray\tZeuabb\tProbEsp_C2bs\tIdScore\tIdProb\tIdV\tConfV\tSession\tTimeNum\tIdExtrap\tTypeE\n+Car470026-2017-Pass1-Z1-CEN2-S2U17907_20170620_212736_466\tnoise\t0\t3.4\t8\t0.54\tpiaf, Tetvir, Tadten, 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|
| b |
| diff -r 000000000000 -r 8c472c4f1bf5 test-data/IdCor2Layer_Test1_out.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/IdCor2Layer_Test1_out.tabular Wed Mar 13 11:18:58 2019 -0400 |
| b |
| b'@@ -0,0 +1,1120 @@\n+nom du 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|
| b |
| diff -r 000000000000 -r 8c472c4f1bf5 vigiechiro_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vigiechiro_macros.xml Wed Mar 13 11:18:58 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> |