| Previous changeset 1:775809e2f6c8 (2019-04-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro commit 4707473e9991d095310f475a54e041c95accd873 |
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modified:
BilanEnrichiPF.R BilanEnrichiPFen.xml SpeciesList.csv |
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added:
test-data/BilanEnrichiPF_Test1_hourly.tabular test-data/BilanEnrichiPF_Test1_nightly.tabular |
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| diff -r 775809e2f6c8 -r 911f80dce38d BilanEnrichiPF.R --- a/BilanEnrichiPF.R Fri Apr 26 12:19:29 2019 -0400 +++ b/BilanEnrichiPF.R Wed Jun 05 13:48:45 2019 -0400 |
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| @@ -21,15 +21,15 @@ -IdC2=fread(args[1]) +IdC2=fread(args[1],encoding="UTF-8") if(substr(IdC2$`nom du fichier`[1],2,2)!="a") { # print("Protocole non conforme, ce script doit etre lance uniquement pour un protocole Point Fixe") print("Wrong protocol, please only use this tool for a \'Point Fixe\' protocol.") }else{ - refPF=fread(args[2]) - GroupList=fread(args[3]) + refPF=fread(args[2],encoding="UTF-8") + GroupList=fread(args[3],encoding="UTF-8") IdC2$ConfV[is.na(IdC2$ConfV)]="" @@ -232,6 +232,6 @@ saveWidget(SummHTMLH,"output-hourly.html") # write.csv2(SummPartH,"output-hourly.tabular",row.names=F) - write.table(SummPartH,"output-hourly.tabular",row.names=F,sep="\n") + write.table(SummPartH,"output-hourly.tabular",row.names=F,sep="\t") } |
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| diff -r 775809e2f6c8 -r 911f80dce38d BilanEnrichiPFen.xml --- a/BilanEnrichiPFen.xml Fri Apr 26 12:19:29 2019 -0400 +++ b/BilanEnrichiPFen.xml Wed Jun 05 13:48:45 2019 -0400 |
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| @@ -48,8 +48,10 @@ <tests> <test> <param name="idc2" value="BilanEnrichiPF_Test1.tabular"/> - <param name="output_choice" value="global"/> + <param name="output_choice" value="global,nightly,hourly"/> <output name="output_summary_tabular" file="BilanEnrichiPF_Test1_out_tab.tabular" ftype="tabular"/> + <output name="output_hourly_tabular" file="BilanEnrichiPF_Test1_hourly.tabular" ftype="tabular"/> + <output name="output_nightly_tabular" file="BilanEnrichiPF_Test1_nightly.tabular" ftype="tabular"/> </test> </tests> <help><![CDATA[ |
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| diff -r 775809e2f6c8 -r 911f80dce38d SpeciesList.csv --- a/SpeciesList.csv Fri Apr 26 12:19:29 2019 -0400 +++ b/SpeciesList.csv Wed Jun 05 13:48:45 2019 -0400 |
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| b"@@ -3,20 +3,20 @@\n Acrsch;piaf;piaf;x;;;x;Acrocephalus schoenobaenus;bird;Phragmite des joncs;Autre\n Acrsci;piaf;piaf;x;;;x;Acrocephalus scirpaceus;bird;Rousserolle effarvatte;Autre\n Acthyp;piaf;piaf;x;;;x;Actitis hypoleucos;bird;Chevalier guignette;Autre\n-Aegcau;piaf;piaf;x;x;x;x;Aegithalos caudatus;bird;M\xe9sange \xe0 longue queue;Autre\n+Aegcau;piaf;piaf;x;x;x;x;Aegithalos caudatus;bird;M\xc3\xa9sange \xc3\xa0 longue queue;Autre\n Alaarv;piaf;piaf;x;;;x;Alauda arvensis;bird;Alouette des champs;Autre\n-Alcatt;piaf;piaf;x;x;x;x;Alcedo atthis;bird;Martin-p\xeacheur d'Europe;Autre\n+Alcatt;piaf;piaf;x;x;x;x;Alcedo atthis;bird;Martin-p\xc3\xaacheur d'Europe;Autre\n Aleruf;piaf;piaf;x;;;x;Alectoris rufa;bird;Perdrix rouge;Autre\n Aloaeg;piaf;piaf;x;;;x;Alopochen aegyptiaca;bird;Ouette d'Egypte;Autre\n amph;amph;amph;x;x;x;x;Amphibia sp.;frog;Amphibien sp.;Autre\n Anacre;piaf;piaf;x;;;x;Anas crecca;bird;Sarcelle d'hiver;Autre\n Anapen;piaf;piaf;x;;;x;Anas penelope;bird;Canard siffleur;Autre\n Anapla;piaf;piaf;x;;;x;Anas platyrhynchos;bird;Canard colvert;Autre\n-Ansans;piaf;piaf;x;;;x;Anser anser;bird;Oie cendr\xe9e;Autre\n-Ansbra;piaf;piaf;x;;;x;Anser brachyrhynchus;bird;Oie \xe0 bec court;Autre\n+Ansans;piaf;piaf;x;;;x;Anser anser;bird;Oie cendr\xc3\xa9e;Autre\n+Ansbra;piaf;piaf;x;;;x;Anser brachyrhynchus;bird;Oie \xc3\xa0 bec court;Autre\n Antcam;piaf;piaf;x;;;;Anthus campestris;bird;Pipit rousseline;Autre\n Antcho;Antcho;Antsp;x;;x;;Antaxius chopardi;bush-cricket;Antaxie catalane;Sauterelle\n-Anthis;Anthis;Antsp;x;;x;;Antaxius hispanicus;bush-cricket;Antaxie pyr\xe9n\xe9enne;Sauterelle\n+Anthis;Anthis;Antsp;x;;x;;Antaxius hispanicus;bush-cricket;Antaxie pyr\xc3\xa9n\xc3\xa9enne;Sauterelle\n Anthiu;Antius;Antsp;x;;x;;Antaxius spinibrachius;bush-cricket;Antaxie voyageuse;Sauterelle\n Antius;Antius;Antsp;x;;x;;Antaxius spinibrachius;bush-cricket;Antaxie voyageuse;Sauterelle\n Antped;Antped;Antsp;x;;;;Antaxius pedestris;bush-cricket;Antaxie marbree;Sauterelle\n@@ -27,45 +27,45 @@\n Antsp;Antsp;Antsp;x;;x;;Antaxius sp.;bush-cricket;Antaxie;Sauterelle\n Anttri;piaf;piaf;x;;;x;Anthus trivialis;bird;Pipit des arbres;Autre\n Apimel;Apimel;Apimel;x;;;x;Apis mellifera;bee;Abeille domestique;Autre\n-Apoagr;Aposp;Mimasp;x;;;;Apodemus agrarius;other mammal;Mulot ray\xe9;Autre\n-Apofla;Aposp;Mimasp;x;x;x;;Apodemus flavicollis;other mammal;Mulot \xe0 collier;Autre\n+Apoagr;Aposp;Mimasp;x;;;;Apodemus agrarius;other mammal;Mulot ray\xc3\xa9;Autre\n+Apofla;Aposp;Mimasp;x;x;x;;Apodemus flavicollis;other mammal;Mulot \xc3\xa0 collier;Autre\n Aposp;Aposp;Mimasp;x;x;x;x;Apodemus sp.;other mammal;Mulot sp.;Autre\n Aposyl;Aposp;Mimasp;x;x;x;x;Apodemus sylvaticus;other mammal;Mulot sylvestre;Autre\n Apuapu;piaf;piaf;x;x;x;x;Apus apus;bird;Martinet noir;Autre\n-Apupal;piaf;piaf;x;;;;Apus pallidus;bird;Martinet p\xe2le;Autre\n-Ardcin;piaf;piaf;x;;;x;Ardea cinerea;bird;H\xe9ron cendr\xe9;Autre\n+Apupal;piaf;piaf;x;;;;Apus pallidus;bird;Martinet p\xc3\xa2le;Autre\n+Ardcin;piaf;piaf;x;;;x;Ardea cinerea;bird;H\xc3\xa9ron cendr\xc3\xa9;Autre\n Arvsap;Arvsp;Arvsp;x;;x;;Arvicola sapidus;other mammal;Campagnol amphibie;Autre\n Arvsch;Arvsp;Arvsp;x;;x;;Arvicola scherman;other mammal;Campagnol fouisseur;Autre\n Arvsp;Arvsp;Arvsp;x;x;x;x;Arvicola sp.;other mammal;Campagnol amphibie/terrestre;Autre\n Arvter;Arvsp;Arvsp;x;x;;x;Arvicola terrestris;other mammal;Campagnol terrestre;Autre\n Asiotu;piaf;piaf;x;;;x;Asio otus;bird;Hibou moyen-duc;Autre\n-Athnoc;piaf;piaf;x;;;x;Athene noctua;bird;Ch\xe9v\xeache d'Ath\xe9na;Autre\n+Athnoc;piaf;piaf;x;;;x;Athene noctua;bird;Ch\xc3\xa9v\xc3\xaache d'Ath\xc3\xa9na;Autre\n Barbar;Barbar;Barbar;x;x;x;x;Barbastella barbastellus;bat;Barbastelle d'Europe;Chauve-souris\n Barfis;Barfis;Barfis;x;;;;Barbitistes fischeri;bush-cricket;Barbitiste languedocien;Sauterelle\n Barsan;Barsan;Barfis;x;;x;;Barbitistes 'sanzii';bush-cricket;Barbitiste cryptique;Sauterelle\n Barser;Barser;Barfis;x;;x;;Barbitistes serricauda;bush-cricket;Barbitiste des bois;Sauterelle\n Bicbic;Bicbic;Metbra;x;;x;;Bicolorana bicolor;bush-cricket;Decticelle bicolore;Sauterelle\n bird;piaf;piaf;;;;x;bird;bird;Oiseau sp.;Autre\n-Bostau;Bostau;Bostau;x;"..b"ush-cricket;Decticelle groupe arboricole;Sauterelle\n Rhibla;Rhibla;Rhibla;;x;;;Rhinolophus blasii;bat;Rhinolophe de Blasius;Chauve-souris\n Rhieur;Rhieur;Rhieur;x;x;x;;Rhinolophus euryale;bat;Rhinolophe euryale;Chauve-souris\n@@ -335,27 +335,27 @@\n SauTurquiesp1;SauTurquiesp1;SauTurquiesp1;;x;;;Tettigoniidae sp. from Turkey 1;bush-cricket;Sauterelle sp. Tu1;Sauterelle\n SauTurquiesp2;SauTurquiesp2;SauTurquiesp2;;x;;;Tettigoniidae sp. from Turkey 2;bush-cricket;Sauterelle sp. Tu2;Sauterelle\n SauTurquiesp3;SauTurquiesp3;SauTurquiesp3;;x;;;Tettigoniidae sp. from Turkey 3;bush-cricket;Sauterelle sp. Tu3;Sauterelle\n-Saxrube;piaf;piaf;x;;;x;Saxicola rubetra;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+Saxrube;piaf;piaf;x;;;x;Saxicola rubetra;bird;Tarier des pr\xc3\xa9s;Autre\n+Saxrubi;piaf;piaf;x;;;x;Saxicola rubicola;bird;Tarier p\xc3\xa2tre;Autre\n+Scorus;piaf;piaf;x;;;x;Scolopax rusticola;bird;B\xc3\xa9casse 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+Sorcor;Mussp;Mussp;x;x;x;x;Soricinus coronatus;other mammal;Musaraigne couronn\xc3\xa9e;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+Sylatr;piaf;piaf;x;x;x;x;Sylvia atricapilla;bird;Fauvette \xc3\xa0 t\xc3\xaate 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+Sylmel;piaf;piaf;x;x;x;x;Sylvia melanocephala;bird;Fauvette m\xc3\xa9lanoc\xc3\xa9phale;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+Tamsib;Tamsib;Tamsib;x;;;;Tamias sibiricus;other mammal;Tamia de Sib\xc3\xa9rie;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@@ -375,10 +375,10 @@\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+Urobre;Urosp;Urosp;x;;;;Uromenus brevicollis;bush-cricket;Ephippig\xc3\xa8re d'Alg\xc3\xa9rie;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+Urosp;Urosp;Urosp;x;x;;;Uromenus sp.;bush-cricket;Ephippig\xc3\xa8re car\xc3\xa9n\xc3\xa9e/d'Alg\xc3\xa9rie;Sauterelle\n+Vanvan;piaf;piaf;x;;;x;Vanellus vanellus;bird;Vanneau hupp\xc3\xa9;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" |
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| diff -r 775809e2f6c8 -r 911f80dce38d test-data/BilanEnrichiPF_Test1_hourly.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/BilanEnrichiPF_Test1_hourly.tabular Wed Jun 05 13:48:45 2019 -0400 |
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| @@ -0,0 +1,20 @@ +"Code" "Groupe" "Nom francais" "Nom scientifique" "Risque d'erreur (%)" "TriGroupe" "19" "20" "21" "22" "23" "00" "01" "02" "03" "04" "05" "06" "07" "08" "09" "10" "11" "12" "13" "14" "15" +"Eptser" "Chauve-souris" "Serotine commune" "Eptesicus serotinus" "3" 3 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 +"Hypsav" "Chauve-souris" "Vespere de Savi" "Hypsugo savii" "60" 3 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"Nyclei" "Chauve-souris" "Noctule de Leisler" "Nyctalus leisleri" "37" 3 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 2 1 +"Pipkuh" "Chauve-souris" "Pipistrelle de Kuhl" "Pipistrellus kuhlii" "3" 3 0 1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"Pipnat" "Chauve-souris" "Pipistrelle de Nathusius" "Pipistrellus nathusii" "51" 3 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"Pippip" "Chauve-souris" "Pipistrelle commune" "Pipistrellus pipistrellus" "1" 3 0 2 8 5 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 +"Pippyg" "Chauve-souris" "Pipistrelle soprane" "Pipistrellus pygmaeus" "11" 3 0 0 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"Rhifer" "Chauve-souris" "Grand Rhinolophe" "Rhinolophus ferrumequinum" "1" 3 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"Rhihip" "Chauve-souris" "Petit Rhinolophe" "Rhinolophus hipposideros" "3" 3 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 +"Confus" "Sauterelle" "Conocephale bigarre" "Conocephalus fuscus" "62" 2 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"Decalb" "Sauterelle" "Dectique a front blanc" "Decticus albifrons" "78" 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 +"Leppun" "Sauterelle" "Sauterelle ponctuee" "Leptophyes punctatissima" "94" 2 0 0 0 0 1 0 3 0 0 0 0 0 1 0 0 0 0 0 0 0 0 +"Phogri" "Sauterelle" "Decticelle cendree" "Pholidoptera griseoaptera" "92" 2 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 3 0 0 +"Plaint" "Sauterelle" "Decticelle intermediaire" "Platycleis intermedia" "92" 2 0 0 1 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"Testes" "Sauterelle" "Decticelle carroyee" "Tessellana tessellata" "85" 2 0 0 0 0 2 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"Tetvir" "Sauterelle" "Sauterelle verte" "Tettigonia viridissima" "64" 2 0 0 0 1 2 1 3 0 0 0 0 0 0 3 1 0 2 0 0 3 1 +"Yerray" "Sauterelle" "Decticelle frele" "Yersinella raymondii" "91" 2 0 0 0 0 2 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"noise" "Autre" "bruit" "noise" "1" 1 3 7 8 23 118 43 36 4 3 8 23 4 8 197 219 407 249 185 259 344 147 +"piaf" "Autre" "Oiseau sp." "Aves sp." "1" 1 32 0 0 0 0 1 3 0 0 1 0 1 1 42 15 41 13 8 25 19 2 |
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| diff -r 775809e2f6c8 -r 911f80dce38d test-data/BilanEnrichiPF_Test1_nightly.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/BilanEnrichiPF_Test1_nightly.tabular Wed Jun 05 13:48:45 2019 -0400 |
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| @@ -0,0 +1,20 @@ +"Code" "Groupe" "Nom francais" "Nom scientifique" "Risque d'erreur (%)" "TriGroupe" "16" "17" "18" "16/03/2019.y" "17/03/2019.y" "18/03/2019.y" +"Eptser" "Chauve-souris" "Serotine commune" "Eptesicus serotinus" "3" 3 2 0 0 1 NA NA +"Hypsav" "Chauve-souris" "Vespere de Savi" "Hypsugo savii" "60" 3 1 0 0 1 NA NA +"Nyclei" "Chauve-souris" "Noctule de Leisler" "Nyctalus leisleri" "37" 3 0 4 0 NA 2 NA +"Pipkuh" "Chauve-souris" "Pipistrelle de Kuhl" "Pipistrellus kuhlii" "3" 3 4 0 0 1 NA NA +"Pipnat" "Chauve-souris" "Pipistrelle de Nathusius" "Pipistrellus nathusii" "51" 3 1 0 0 1 NA NA +"Pippip" "Chauve-souris" "Pipistrelle commune" "Pipistrellus pipistrellus" "1" 3 15 2 0 1 1 NA +"Pippyg" "Chauve-souris" "Pipistrelle soprane" "Pipistrellus pygmaeus" "11" 3 4 0 0 2 NA NA +"Rhifer" "Chauve-souris" "Grand Rhinolophe" "Rhinolophus ferrumequinum" "1" 3 1 1 0 1 1 NA +"Rhihip" "Chauve-souris" "Petit Rhinolophe" "Rhinolophus hipposideros" "3" 3 2 0 0 2 NA NA +"Confus" "Sauterelle" "Conocephale bigarre" "Conocephalus fuscus" "62" 2 0 1 0 NA 1 NA +"Decalb" "Sauterelle" "Dectique a front blanc" "Decticus albifrons" "78" 2 0 1 0 NA 1 NA +"Leppun" "Sauterelle" "Sauterelle ponctuee" "Leptophyes punctatissima" "94" 2 0 5 0 NA 1 NA +"Phogri" "Sauterelle" "Decticelle cendree" "Pholidoptera griseoaptera" "92" 2 1 4 0 1 2 NA +"Plaint" "Sauterelle" "Decticelle intermediaire" "Platycleis intermedia" "92" 2 1 2 0 1 1 NA +"Testes" "Sauterelle" "Decticelle carroyee" "Tessellana tessellata" "85" 2 0 3 0 NA 2 NA +"Tetvir" "Sauterelle" "Sauterelle verte" "Tettigonia viridissima" "64" 2 3 11 3 1 2 1 +"Yerray" "Sauterelle" "Decticelle frele" "Yersinella raymondii" "91" 2 0 3 0 NA 2 NA +"noise" "Autre" "bruit" "noise" "1" 1 440 1598 257 1 2 1 +"piaf" "Autre" "Oiseau sp." "Aves sp." "1" 1 94 92 18 2 2 2 |