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Remvoe genus
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damianooldoni committed Dec 22, 2023
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1 change: 0 additions & 1 deletion data/processed/alert_species.csv
Original file line number Diff line number Diff line change
Expand Up @@ -111,7 +111,6 @@ Robinia pseudoacacia,5352251
Acer negundo,3189866
Arundo donax,2703041
Azolla filiculoides,2650107
Carpobrotus,3084841
Cotoneaster horizontalis,3025617
Elaeagnus angustifolia,3039269
Elodea canadensis,2865448
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140 changes: 140 additions & 0 deletions data/reference/Species-2023-12-22.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,140 @@
id,name,vernacular_name,vernacular_name_en,vernacular_name_fr,vernacular_name_nl,gbif_taxon_key,tags
81,Acacia saligna,wilgacacia,golden wreath wattle,mimosa bleuâtre,wilgacacia,2978552,"1,3"
115,Acer negundo,vederesdoorn,box elder,érable negundo,vederesdoorn,3189866,"1,42"
73,Acridotheres tristis,treurmaina,common myna,martin triste,treurmaina,2489005,"3,5,8"
85,Ailanthus altissima,hemelboom,tree of heaven,ailante glanduleux,hemelboom,3190653,"1,3,42"
54,Alopochen aegyptiacus,nijlgans,Egyptian goose,ouette d'Égypte,nijlgans,2498252,"3,5,8"
97,Alternanthera philoxeroides,alligatorkruid,alligator weed,herbe à alligator,alligatorkruid,3084923,"1,3,42"
74,Ameiurus melas,zwarte dwergmeerval,black bullhead,poisson-chat commun,zwarte dwergmeerval,2340977,"3,5,11"
83,Andropogon virginicus,Amerikaans bezemgras,broomsedge bluestem,barbon de Virginie,Amerikaans bezemgras,2706080,"1,3"
31,Aponogeton distachyos,Kaapse waterlelie,Cape pondweed,Aponogeton à deux épis,Kaapse waterlelie,5328593,"1,2,42"
47,Arthurdendyus triangulatus,nieuw-Zeelandse platworm,New Zealand flatworm,ver plat de Nouvelle-Zélande,nieuw-Zeelandse platworm,2502792,"3,5,12"
116,Arundo donax,pijlriet,giant reed,canne du Languedoc,pijlriet,2703041,"1,42"
96,Asclepias syriaca,zijdeplant,common milkweed,asclépiade de Syrie,zijdeplant,3170247,"1,3,42"
63,Axis axis,axishert,axis deer,cerf axis,axishert,2440934,"3,5,6"
117,Azolla filiculoides,grote kroosvaren,water fern,fougère d'eau,grote kroosvaren,2650107,"1,42"
95,Baccharis halimifolia,struikaster,Eastern baccharis,séneçon en arbre,struikaster,3129663,"1,3,42"
13,Cabomba caroliniana,waterwaaier,Fanwort,cabomba de Caroline,waterwaaier,2882443,"1,2,3,42"
57,Callosciurus erythraeus,Pallas eekhoorn,Pallas' squirrel,écureuil de Pallas,Pallas eekhoorn,2437394,"3,5,6"
35,Callosciurus finlaysonii,Thaise eekhoorn,Finlayson's squirrel,écureuil de Finlayson,Thaise eekhoorn,2437399,"3,5,6"
91,Cardiospermum grandiflorum,ballonrank,Balloon vine,corinde à grandes fleurs,ballonrank,3189935,"1,3"
93,Celastrus orbiculatus,Aziatische Boomwurger,Oriental bittersweet,célastre asiatique,Aziatische Boomwurger,3169169,"1,3"
52,Channa argus,noordelijke slangekopvis,northern snakehead,poisson à tête de serpent,noordelijke slangekopvis,4284921,"3,5,11"
22,Cherax destructor,gewone yabby,Common yabby,,gewone yabby,4417558,"2,4,5"
92,Cortaderia jubata,hoog pampasgras,Purple pampas grass,herbe de la pampa pourpre,hoog pampasgras,2704521,"1,3"
37,Corvus splendens,huiskraai,Indian house crow,corbeau familier,huiskraai,2482499,"3,5,8"
119,Cotoneaster horizontalis,vlakke dwergmispel,wall cotoneaster,cotonéaster rampant,vlakke dwergmispel,3025617,"1,42"
29,Crassula helmsii,watercrassula,,,watercrassula,5362054,"1,2"
32,Egeria densa,egeria,Large-flowered waterweed,Egeria,egeria,5329263,"1,2,42"
78,Ehrharta calycina,roze rimpelgras,Perrenial veldt grass,ehrharte calicinale,roze rimpelgras,2702865,"1,3"
87,Eichhornia crassipes,waterhyacint,Water hyacinth,jacinthe d'eau,waterhyacint,2765942,"1,3,42"
120,Elaeagnus angustifolia,smalle olijfwilg,Russian olive,olivier de Bohême,smalle olijfwilg,3039269,"1,42"
121,Elodea canadensis,brede waterpest,American waterweed,élodée du Canada,brede waterpest,2865448,"1,42"
98,Elodea nuttallii,smalle waterpest,Nuttall's waterweed,élodée de Nuttall,smalle waterpest,5329212,"1,3,42"
39,Eriocheir sinensis,Chinese wolhandkrab,Chinese mittencrab,crabe chinois,Chinese wolhandkrab,2225776,"3,5,9"
26,Erythranthe guttata,gele maskerbloem,monkeyflower,,gele maskerbloem,7346102,"1,2"
122,Fallopia baldschuanica,Chinese bruidssluier,Russian-vine,vrillée du Turkestan,Chinese bruidssluier,5334351,"1,42"
20,Faxonius immunis,calicotrivierkreeft,Calico crayfish,Ecrevisse Calicot,calicotrivierkreeft,8930656,"2,4,5"
21,Faxonius juvenilis,Kentuckyrivierkreeft,Kentucky River crayfish,,Kentuckyrivierkreeft,8721209,"2,4,5"
60,Faxonius limosus,gevlekte rivierkreeft,Spiny-cheek crayfish,écrevisse américaine,gevlekte rivierkreeft,8909595,"3,4,5"
19,Faxonius rusticus,roestbruine Amerikaanse Rivierkreeft,rusty crayfish,écrevisse à taches rouges,roestbruine Amerikaanse Rivierkreeft,8979506,"2,3,4,5"
17,Faxonius virilis,geknobbelde Amerikaanse rivierkreeft,Virile crayfish,écrevisse à pinces bleues,geknobbelde Amerikaanse rivierkreeft,8971201,"2,3,4,5"
123,Fraxinus pennsylvanica,Pennsylvaanse es,green ash,frêne rouge,Pennsylvaanse es,3172348,"1,42"
71,Fundulus heteroclitus,mummichog,mummichog,choquemort,mummichog,5712056,"3,5,11"
43,Gambusia affinis,westelijk muskietenvisje,western mosquitofish,gambusie de l’ouest,westelijk muskietenvisje,2350580,"3,5,11"
62,Gambusia holbrooki,oostelijk muskietenvisje,eastern mosquitofish,gambusie de l’est,oostelijk muskietenvisje,2350570,"3,5,11"
77,Gunnera tinctoria,gewone gunnera,Chilean rhubarb,rhubarbe géante du Chili,gewone gunnera,2984306,"1,3"
76,Gymnocoronis spilanthoides,smalle theeplant,Senegal tea plant,faux hygrophile,smalle theeplant,6063677,"1,3,42"
79,Hakea sericea,hakea,bushy needlewood,hakéa soyeux,hakea,7287606,"1,3"
125,Helianthus laetiflorus,stijve zonnebloem,cheerful sunflower,tournesol vivace,stijve zonnebloem,3119181,"1,42"
124,Helianthus tuberosus,aardpeer,Jerusalem artichoke,topinambour,aardpeer,3119175,"1,42"
2,Heracleum mantegazzianum,reuzenberenklauw,Giant hogweed,berce du Caucase,reuzenberenklauw,3034825,"1,2,3,42"
14,Heracleum persicum,Perzische berenklauw,Persian hogweed,berce de Perse,Perzische berenklauw,3628745,"1,2,3"
15,Heracleum sosnowskyi,Sosnowsky's berenklauw,Sosnowsky's hogweed,berce de Sosnowsky,Sosnowsky's berenklauw,3642949,"1,2,3"
64,Herpestes javanicus,Indische mangoeste,Small Asian mongoose,mangouste,Indische mangoeste,2434271,"3,5,6"
25,Houttuynia cordata,moerasanemoon,Chameleon plant,Poivre de Chine,moerasanemoon,5384931,"1,2"
88,Humulus scandens,oosterse hop,Japanese hop,houblon du Japon,oosterse hop,2984537,"1,3"
126,Hydrilla verticillata,Florida elodea,Florida elodea,,,5329570,"1,42"
3,Hydrocotyle ranunculoides,grote waternavel,Floating pennywort,hydrocotyle fausse-renoncule,grote waternavel,7978544,"1,2,3,42"
127,Impatiens capensis,oranje springzaad,orange jewelweed,impatiente du Cap,oranje springzaad,2891774,"1,42"
5,Impatiens glandulifera,reuzenbalsemien,Himalayan balsam,balsamine de l'Himalaya,reuzenbalsemien,2891770,"1,2,3,42"
34,Koenigia polystachya,Afghaanse duizendknoop,Himalayan knotweed,renouée à nombreux épis,Afghaanse duizendknoop,8848208,"1,2,3,42"
128,Laburnum anagyroides,goudenregen,golden rain,cytise faux ébénier,goudenregen,5356345,"1,42"
9,Lagarosiphon major,verspreidbladige waterpest,Curly waterweed,élodée à feuilles alternes,verspreidbladige waterpest,2865565,"1,2,3,42"
67,Lampropeltis getula,koningsslang,common kingsnake,serpent roi de Californie,koningsslang,9799308,"3,5,13"
129,Lemna minuta,dwergkroos,least duckweed,lentille d’eau minuscule,dwergkroos,2867614,"1,42"
130,Lemna turionifera,knopkroos,turion duckweed,lentille d'eau rouge,knopkroos,2867631,"1,42"
46,Lepomis gibbosus,zonnebaars,Pumpkinseed,perche soleil,zonnebaars,2394486,"3,5,11"
86,Lespedeza cuneata,Chinese struikklaver,Chinese bushclover,lespédéza soyeux,Chinese struikklaver,8114276,"1,3"
131,Limnobium laevigatum,Amazone kikkerbeet,West Indian spongeplant,grenouillette,Amazone kikkerbeet,11055820,"1,42"
36,Limnoperna fortunei,gouden mossel,golden mussel,moule pygmée,gouden mossel,5855350,"3,5,7"
69,Lithobates catesbeianus,Amerikaanse stierkikker,American bullfrog,grenouille taureau,Amerikaanse stierkikker,2427091,"3,5,14"
4,Ludwigia grandiflora,waterteunisbloem,Water-primrose,jussie à grandes fleurs,waterteunisbloem,5421039,"1,2,3,42"
16,Ludwigia peploides,kleine waterteunisbloem,Floating primrose-willow,jussie rampante,kleine waterteunisbloem,5420991,"1,2,3,42"
84,Lygodium japonicum,Japanse klimvaren,Vine-like fern,fougère grimpante du Japon,Japanse klimvaren,2650436,"1,3"
10,Lysichiton americanus,moerasaronskelk,American skunk cabbage,faux arum,moerasaronskelk,2869311,"1,2,3"
136,Mahonia aquifolium,mahonie,Oregon grape,mahonia faux houx,mahonie,3033865,"1,42"
99,Microstegium vimineum,Japans steltgras,Japanese stiltgrass,herbe à échasses japonaise,Japans steltgras,5289808,"1,3"
105,Morone americana,Amerikaanse baars,white perch,bar blanc d’Amérique,Amerikaanse baars,2394604,"3,5,11"
45,Muntiacus reevesi,Chinese muntjak,Muntjac deer,muntjac de Chine,Chinese muntjak,2440946,"3,5,6"
59,Myocastor coypus,beverrat,Coypu,ragondin,beverrat,4264680,"3,5,6"
6,Myriophyllum aquaticum,parelvederkruid,Parrot's feather,myriophylle du Brésil,parelvederkruid,5361785,"1,2,3,42"
11,Myriophyllum heterophyllum,ongelijkbladig vederkruid,Broadleaf watermilfoil,myriophylle hétérophylle,ongelijkbladig vederkruid,5361762,"1,2,3,42"
133,Myriophyllum rubricaule,rossig vederkruid,,,rossig vederkruid,11742641,"1,42"
55,Nasua nasua,neusbeer,coati,coati roux Roter,neusbeer,2433536,"3,5,6"
66,Nyctereutes procyonoides,wasbeerhond,Raccoon dog,chien viverrin,wasbeerhond,2434552,"3,5,6"
58,Ondatra zibethicus,muskusrat,Muskrat,rat musqué,muskusrat,5219858,"3,5,6"
68,Oxyura jamaicensis,rosse stekelstaart,Ruddy duck,érismature rousse,rosse stekelstaart,2498305,"3,5,8"
40,Pacifastacus leniusculus,Californische rivierkreeft,Signal crayfish,écrevisse signal,Californische rivierkreeft,2226990,"3,4,5"
94,Parthenium hysterophorus,schijnambrosia,Whitetop weed,fausse camomille,schijnambrosia,3086784,"1,3"
137,Parthenocissus inserta,valse wingerd,thicket creeper,vigne vierge commune,valse wingerd,3039203,"1,42"
107,Parthenocissus quinquefolia,vijfbladige wingerd,Virginia creeper,vigne-vierge vraie,vijfbladige wingerd,3039194,"1,42"
135,Parthenocissus tricuspidata,Oosterse wingerd,Boston ivy,vigne-vierge à trois pointes,Oosterse wingerd,3039209,"1,42"
80,Pennisetum setaceum,fraai lampenpoetsersgras,Crimson fountaingrass,herbe aux écouvillons pourpres,fraai lampenpoetsersgras,5828232,"1,3"
70,Perccottus glenii,amoergrondel,Amur sleeper,goujon de l'amour,amoergrondel,2390064,"3,5,11"
101,Persicaria perfoliata,gestekelde duizendknoop,Asiatic tearthumb,renouée perfoliée,gestekelde duizendknoop,4033648,"1,3"
28,Petasites japonicus,Japans hoefblad,Giant butterbur,pétasite du Japon,Japans hoefblad,3088310,"1,2"
100,Pistia stratiotes,watersla,water lettuce,laitue d’eau,watersla,2870583,"1,3,42"
51,Plotosus lineatus,gestreepte koraalmeerval,Striped eel catfish,poisson-chat-rayé,gestreepte koraalmeerval,7965247,"3,5,11"
30,Pontederia cordata,snoekkruid,pickerel weed,pontédérie à feuilles en cœur,snoekkruid,2766030,"1,2"
23,Procambarus acutus,gestreepte Amerikaanse rivierkreeft,white river crayfish,Écrevisse blanche de rivière,gestreepte Amerikaanse rivierkreeft,2227289,"2,4,5"
12,Procambarus clarkii,rode Amerikaanse rivierkreeft,Red swamp crayfish,écrevisse de Louisiane,rode Amerikaanse rivierkreeft,2227300,"2,3,4,5"
33,Procambarus virginalis,marmerkreeft,Marbled crayfish,écrevisse marbrée,marmerkreeft,9442269,"2,3,4,5"
56,Procyon lotor,wasbeer,raccoon,raton laveur,wasbeer,5218786,"3,5,6"
82,Prosopis juliflora,mesquite,Mesquite,bayahonde,mesquite,5358460,"1,3"
109,Prunus laurocerasus,kerslaurier,cherry laurel,laurier-cerise,kerslaurier,3021496,"1,42"
134,Prunus serotina,Amerikaanse vogelkers,black cherry,cerisier noir,Amerikaanse vogelkers,3021850,"1,42"
44,Pseudorasbora parva,blauwbandgrondel,"Stone moroko, topmouth gudgeon",goujon Asiatique,blauwbandgrondel,2362868,"3,5,11"
90,Pueraria montana lobata,kudzu,Kudzu vine,kudzu,kudzu,2977647,"1,3"
38,Pycnonotus cafer,roodbuikbuulbuul,red-vented bulbul,bulbul à ventre rouge,roodbuikbuulbuul,2486131,"3,5,8"
140,Reynoutria bohemica,Boheemse duizendknoop,Bohemian knotweed,renouée de Bohême,Boheemse duizendknoop,4038485,"1,42"
132,Reynoutria japonica,Japanse duizendknoop,Japanese Knotweed,Renouée du Japon,Japanse duizendknoop,2889173,"1,42"
142,Reynoutria sachalinensis,Sachalinse duizendknoop,giant knotweed,renouée de Sakhaline,Sachalinse duizendknoop,2889088,"1,42"
106,Rhus typhina,fluweelboom,staghorn sumac,sumac vinaigrier,fluweelboom,3190538,"1,42"
114,Robinia pseudoacacia,gewone robinia,black locust,robinier faux-acacia,gewone robinia,5352251,"1,42"
110,Rosa rugosa,rimpelroos,rugosa rose,rosier rugueux,rimpelroos,3003979,"1,42"
113,Rubus armeniacus,dijkviltbraam,Armenian blackberry,ronce d’Arménie,dijkviltbraam,2996525,"1,42"
141,Rudbeckia laciniata,slipbladige rudbeckia,cutleaf coneflower,Rudbéckie laciniée,slipbladige rudbeckia,3114229,"1,42"
103,Rugulopteryx okamurae,stomp gaffelwier,,algue brune du Japon,stomp gaffelwier,5824863,"3,15"
102,Salvinia molesta,grote vlotvaren,kariba weed,salvinie géante,grote vlotvaren,5274863,"1,3,42"
24,Saururus cernuus,Leidse plant,lizard's tail,queue de lézard,Leidse plant,5384932,"1,2"
42,Sciurus carolinensis,grijze eekhoorn,Grey squirrel,écureuil gris,grijze eekhoorn,5219681,"3,5,6"
49,Sciurus niger,Amerikaanse voseekhoorn,Fox squirrel,écureuil fauve,Amerikaanse voseekhoorn,5219683,"3,5,6"
53,Solenopsis geminata,tropische vuurmier,tropical imported fire ant,fourmi de feu tropicale,tropische vuurmier,5035187,"3,5,10"
41,Solenopsis invicta,rode vuurmier,red imported fire ant,grande fourmi de feu,rode vuurmier,5035230,"3,5,10"
48,Solenopsis richteri,zwarte vuurmier,black imported fire ant,fourmi de feu noire,zwarte vuurmier,5035017,"3,5,10"
144,Solidago canadensis,Canadese guldenroede,Canada goldenrod,verge d'or du Canada,Canadese guldenroede,5389029,"1,42"
112,Solidago gigantea,late guldenroede,giant goldenrod,solidage géant,late guldenroede,5389017,"1,42"
111,Spiraea alba,witte spirea,meadowsweet,spirée blanche,witte spirea,3026585,"1,42"
108,Spiraea billardii,spierstruik,billard's Bridewort,spirée de Billiard,spierstruik,7889822,"1,42"
139,Spiraea douglasii,Douglasspirea,hardhack steeplebush,spirée de Douglas,Douglasspirea,3027159,"1,42"
143,Spiraea salicifolia,theeboompje,bridewort,spirée à feuilles de saule,theeboompje,3026454,"1,42"
138,Spiraea tomentosa,viltige pluimspirea,steeplebush,spirée tomenteuse,viltige pluimspirea,3026819,"1,42"
65,Tamias sibiricus,Siberische grondeekhoorn,Siberian chipmunk,tamia de Sibérie,Siberische grondeekhoorn,2437450,"3,5,6"
104,Threskiornis aethiopicus,heilige ibis,Sacred ibis,ibis sacré,heilige ibis,2480764,"3,5,8"
50,Trachemys scripta,lettersierschildpad,"Red-eared, yellow-bellied and Cumberland sliders",tortue de Floride,lettersierschildpad,2443002,"3,5,13"
89,Triadica sebifera,talgboom,Chinese tallow,arbre à suif,talgboom,3054399,"1,3"
75,Vespa velutina,Aziatische hoornaar,yellow-legged hornet,frelon asiatique,Aziatische hoornaar,1311477,"3,5,10"
61,Wasmannia auropunctata,dwergvuurmier,little fire ant,petite fourmi de feu,dwergvuurmier,1315391,"3,5,10"
72,Xenopus laevis,Afrikaanse klauwkikker,African clawed frog,xénope lisse,Afrikaanse klauwkikker,5217334,"3,5,14"
27,Zizania latifolia,wilde rijst,Manchurian wild rice,riz sauvage de Mandchourie,wilde rijst,10919373,"1,2"
10 changes: 9 additions & 1 deletion src/retrieve_compare_taxon_keys.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ Create a data frame `input_data` from the export of the species list used in the

```{r read_species_list}
input_data <- read_csv(
file = here("data", "reference", "Species-2023-12-21.csv")
file = here("data", "reference", "Species-2023-12-22.csv")
)
```

Expand Down Expand Up @@ -152,6 +152,14 @@ taxa_checklists <- taxa_checklists %>%

This mismatch has been reported to GBIF (see issue [4946] (https://github.com/gbif/portal-feedback/issues/4946)). Once solved, this patch can be removed.

### Remove genera

At the moment the GBIF-Alert doesn't support genera or higher taxon keys. See more details on issue [274](https://github.com/riparias/gbif-alert/issues/274). We remove `Carpobrotus`, originally included in the DVW priority species list:

```{r}
taxa_checklists <- taxa_checklists %>% filter(.data$canonicalName != "Carpobrotus")
```

## Higher rank

The Asian hornet (_Vespa velutina_) is mentioned in the List of Invasive Alien Species of Union concern as a subspecies: _Vespa velutina nigrithorax_:
Expand Down

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