This package is designed to simplify the workflow of combining amphibian data sets from sources that use different taxonomic nomenclature, by conforming to the most current system suggested by the Amphibian Species of the World: an Online Resource, Forst (2017). Comparative studies require the combination of data from a range of sources such as spatial or conservation data from the IUCN red list, information on evolutionary history from published a phylogeny such as Pyron 2014, Syst Biol or life history data from AnAge. These sources have either made the decision to follow a specific taxonomic system or, more often, are no longer up-to-date. It can therefore be complicated to establish a universal or current nomenclature to be able to efficiently combine data sets. As such, the main objective of this package is to harvest taxonomic classifications of all amphibian species listed on the ASW website, harvest all listed synonyms per species and then using this information, suggest ASW names for any given list of taxa.
This package could also be useful for easily updating museum catalogs etc., and includes functions for producing summary statistics on species numbers at various taxonomic levels, or to update species names in manuscripts etc. after a taxonomic group has received nomenclature revisions.
Below are some examples of how to use the package. (REMEMBER! Please cite not only AmphiNom but all data resources used, including the Amphibian Species of the World).
AmphiNom is a package written in the R programming language. The most recent version can be downloaded from ‘gitHub’, using the ‘devtools’ library. The first step is therefore to make sure that the ‘devtools’ package is installed and loaded. Successful installation of ‘AmphiNom’ might also require that the ‘XML’ package is installed prior.
The starting point of this package is to populate a list of all currently registered species on the ASW website. For ease-of-use, a version of this is stored in the ‘AmphiNom’ package internally, but this may of course be outdated and so to generate your own, up-to-date version run the getTaxonomy() function.The function takes no arguments and essentially iterates through the ASW website, building the URL for each species through a bottom-up approach (i.e. first looking for all orders, then superfamilies, then families, subfamilies, genera and finally species). The resulting table contains 7 columns: one for each taxonomic level (Order through to Species) and a final column with the URL for the ASW website for each species.
Run the getTaxonomy() function (this may take 10 to 15 minutes), or have a look at the internally stored ‘asw_taxonomy’ data file:
The first think one might be interested in is to get some basic numbers for listed taxonomic units nested within a particular level.
| number_of_units | |
|---|---|
| Oders | 0 |
| Families | 0 |
| Genera | 0 |
| Species | 0 |
Additional arguments can be specified in the aswStats() function to narrow down the search. For example to get information on only a specific Family:
| number_of_units | |
|---|---|
| Oders | 0 |
| Families | 0 |
| Genera | 0 |
| Species | 0 |
This can be applied to any taxonomic level and to make sure everything is working properly (or if the asw_taxonomy data-set is up-to-date), you could double check if this matches the information on the ASW website
We can also turn on ‘verbose’ to get a list of all nested units instead of just the summary a table. This is useful for getting a more detailed overview, but also for making graphical representations of this information:
## $Orders
##
## Caudata
## 490
##
## $Super_families
## < table of extent 0 >
##
## $Families
##
## Plethodontidae
## 490
##
## $Sub_families
##
## Hemidactyliinae Plethodontinae
## 384 106
##
## $Genera
##
## Aneides Aquiloeurycea Batrachoseps Bolitoglossa Bradytriton
## 10 6 21 136 1
## Chiropterotriton Cryptotriton Dendrotriton Desmognathus Ensatina
## 23 7 8 24 1
## Eurycea Gyrinophilus Hemidactylium Hydromantes Isthmura
## 32 4 1 5 7
## Ixalotriton Karsenia Nototriton Nyctanolis Oedipina
## 2 1 20 1 40
## Parvimolge Phaeognathus Plethodon Pseudoeurycea Pseudotriton
## 1 1 56 40 3
## Speleomantes Stereochilus Thorius Urspelerpes
## 8 1 29 1
##
## $Species
## [1] "Aquiloeurycea cafetalera" "Aquiloeurycea cephalica"
## [3] "Aquiloeurycea galeanae" "Aquiloeurycea praecellens"
## [5] "Aquiloeurycea quetzalanensis" "Aquiloeurycea scandens"
## [7] "Batrachoseps altasierrae" "Batrachoseps attenuatus"
## [9] "Batrachoseps bramei" "Batrachoseps campi"
## [11] "Batrachoseps diabolicus" "Batrachoseps gabrieli"
## [13] "Batrachoseps gavilanensis" "Batrachoseps gregarius"
## [15] "Batrachoseps incognitus" "Batrachoseps kawia"
## [17] "Batrachoseps luciae" "Batrachoseps major"
## [19] "Batrachoseps minor" "Batrachoseps nigriventris"
## [21] "Batrachoseps pacificus" "Batrachoseps regius"
## [23] "Batrachoseps relictus" "Batrachoseps robustus"
## [25] "Batrachoseps simatus" "Batrachoseps stebbinsi"
## [27] "Batrachoseps wrighti" "Bolitoglossa altamazonica2"
## [29] "Bolitoglossa adspersa" "Bolitoglossa alberchi"
## [31] "Bolitoglossa altamazonica" "Bolitoglossa alvaradoi"
## [33] "Bolitoglossa anthracina" "Bolitoglossa aurae"
## [35] "Bolitoglossa aureogularis" "Bolitoglossa awajun"
## [37] "Bolitoglossa biseriata" "Bolitoglossa borburata"
## [39] "Bolitoglossa bramei" "Bolitoglossa caldwellae"
## [41] "Bolitoglossa capitana" "Bolitoglossa carri"
## [43] "Bolitoglossa cataguana" "Bolitoglossa celaque"
## [45] "Bolitoglossa centenorum" "Bolitoglossa cerroensis"
## [47] "Bolitoglossa chica" "Bolitoglossa chinanteca"
## [49] "Bolitoglossa chucantiensis" "Bolitoglossa coaxtlahuacana"
## [51] "Bolitoglossa colonnea" "Bolitoglossa compacta"
## [53] "Bolitoglossa conanti" "Bolitoglossa copia"
## [55] "Bolitoglossa copinhorum" "Bolitoglossa cuchumatana"
## [57] "Bolitoglossa cuna" "Bolitoglossa daryorum"
## [59] "Bolitoglossa decora" "Bolitoglossa diaphora"
## [61] "Bolitoglossa digitigrada" "Bolitoglossa diminuta"
## [63] "Bolitoglossa dofleini" "Bolitoglossa dunni"
## [65] "Bolitoglossa engelhardti" "Bolitoglossa epimela"
## [67] "Bolitoglossa equatoriana" "Bolitoglossa eremia"
## [69] "Bolitoglossa flavimembris" "Bolitoglossa flaviventris"
## [71] "Bolitoglossa franklini" "Bolitoglossa gomezi"
## [73] "Bolitoglossa gracilis" "Bolitoglossa guaneae"
## [75] "Bolitoglossa guaramacalensis" "Bolitoglossa hartwegi"
## [77] "Bolitoglossa heiroreias" "Bolitoglossa helmrichi"
## [79] "Bolitoglossa hermosa" "Bolitoglossa hiemalis"
## [81] "Bolitoglossa huehuetenanguensis" "Bolitoglossa hypacra"
## [83] "Bolitoglossa indio" "Bolitoglossa insularis"
## [85] "Bolitoglossa jacksoni" "Bolitoglossa jugivagans"
## [87] "Bolitoglossa kamuk" "Bolitoglossa kaqchikelorum"
## [89] "Bolitoglossa la" "Bolitoglossa leandrae"
## [91] "Bolitoglossa lignicolor" "Bolitoglossa lincolni"
## [93] "Bolitoglossa longissima" "Bolitoglossa lozanoi"
## [95] "Bolitoglossa macrinii" "Bolitoglossa madeira"
## [97] "Bolitoglossa magnifica" "Bolitoglossa marmorea"
## [99] "Bolitoglossa medemi" "Bolitoglossa meliana"
## [101] "Bolitoglossa mexicana" "Bolitoglossa minutula"
## [103] "Bolitoglossa mombachoensis" "Bolitoglossa morio"
## [105] "Bolitoglossa mucuyensis" "Bolitoglossa mulleri"
## [107] "Bolitoglossa nicefori" "Bolitoglossa nigrescens"
## [109] "Bolitoglossa ninadormida" "Bolitoglossa nussbaumi"
## [111] "Bolitoglossa nympha" "Bolitoglossa oaxacensis"
## [113] "Bolitoglossa obscura" "Bolitoglossa occidentalis"
## [115] "Bolitoglossa odonnelli" "Bolitoglossa omniumsanctorum"
## [117] "Bolitoglossa oresbia" "Bolitoglossa orestes"
## [119] "Bolitoglossa pacaya" "Bolitoglossa palmata"
## [121] "Bolitoglossa pandi" "Bolitoglossa paraensis"
## [123] "Bolitoglossa peruviana" "Bolitoglossa pesrubra"
## [125] "Bolitoglossa phalarosoma" "Bolitoglossa platydactyla"
## [127] "Bolitoglossa porrasorum" "Bolitoglossa psephena"
## [129] "Bolitoglossa pygmaea" "Bolitoglossa ramosi"
## [131] "Bolitoglossa riletti" "Bolitoglossa robinsoni"
## [133] "Bolitoglossa robusta" "Bolitoglossa rostrata"
## [135] "Bolitoglossa rufescens" "Bolitoglossa salvinii"
## [137] "Bolitoglossa savagei" "Bolitoglossa schizodactyla"
## [139] "Bolitoglossa silverstonei" "Bolitoglossa sima"
## [141] "Bolitoglossa sombra" "Bolitoglossa sooyorum"
## [143] "Bolitoglossa splendida" "Bolitoglossa striatula"
## [145] "Bolitoglossa stuarti" "Bolitoglossa subpalmata"
## [147] "Bolitoglossa suchitanensis" "Bolitoglossa synoria"
## [149] "Bolitoglossa tamaense" "Bolitoglossa tapajonica"
## [151] "Bolitoglossa tatamae" "Bolitoglossa taylori"
## [153] "Bolitoglossa tenebrosa" "Bolitoglossa tica"
## [155] "Bolitoglossa tzultacaj" "Bolitoglossa vallecula"
## [157] "Bolitoglossa veracrucis" "Bolitoglossa walkeri"
## [159] "Bolitoglossa xibalba" "Bolitoglossa yariguiensis"
## [161] "Bolitoglossa yucatana" "Bolitoglossa zacapensis"
## [163] "Bolitoglossa zapoteca" "Bradytriton silus"
## [165] "Chiropterotriton arboreus" "Chiropterotriton aureus"
## [167] "Chiropterotriton casasi" "Chiropterotriton ceronorum"
## [169] "Chiropterotriton chico" "Chiropterotriton chiropterus"
## [171] "Chiropterotriton chondrostega" "Chiropterotriton cieloensis"
## [173] "Chiropterotriton cracens" "Chiropterotriton dimidiatus"
## [175] "Chiropterotriton infernalis" "Chiropterotriton lavae"
## [177] "Chiropterotriton magnipes" "Chiropterotriton melipona"
## [179] "Chiropterotriton miquihuanus" "Chiropterotriton mosaueri"
## [181] "Chiropterotriton multidentatus" "Chiropterotriton nubilus"
## [183] "Chiropterotriton orculus" "Chiropterotriton perotensis"
## [185] "Chiropterotriton priscus" "Chiropterotriton terrestris"
## [187] "Chiropterotriton totonacus" "Cryptotriton alvarezdeltoroi"
## [189] "Cryptotriton monzoni" "Cryptotriton nasalis"
## [191] "Cryptotriton necopinus" "Cryptotriton sierraminensis"
## [193] "Cryptotriton veraepacis" "Cryptotriton xucaneborum"
## [195] "Dendrotriton bromeliacius" "Dendrotriton chujorum"
## [197] "Dendrotriton cuchumatanus" "Dendrotriton kekchiorum"
## [199] "Dendrotriton megarhinus" "Dendrotriton rabbi"
## [201] "Dendrotriton sanctibarbarus" "Dendrotriton xolocalcae"
## [203] "Eurycea aquatica" "Eurycea bislineata"
## [205] "Eurycea braggi" "Eurycea chamberlaini"
## [207] "Eurycea chisholmensis" "Eurycea cirrigera"
## [209] "Eurycea guttolineata" "Eurycea hillisi"
## [211] "Eurycea junaluska" "Eurycea latitans"
## [213] "Eurycea longicauda" "Eurycea lucifuga"
## [215] "Eurycea multiplicata" "Eurycea nana"
## [217] "Eurycea naufragia" "Eurycea neotenes"
## [219] "Eurycea nerea" "Eurycea paludicola"
## [221] "Eurycea pterophila" "Eurycea quadridigitata"
## [223] "Eurycea rathbuni" "Eurycea robusta"
## [225] "Eurycea sosorum" "Eurycea spelaea"
## [227] "Eurycea sphagnicola" "Eurycea subfluvicola"
## [229] "Eurycea tonkawae" "Eurycea troglodytes"
## [231] "Eurycea tynerensis" "Eurycea wallacei"
## [233] "Eurycea waterlooensis" "Eurycea wilderae"
## [235] "Gyrinophilus gulolineatus" "Gyrinophilus palleucus"
## [237] "Gyrinophilus porphyriticus" "Gyrinophilus subterraneus"
## [239] "Hemidactylium scutatum" "Isthmura bellii"
## [241] "Isthmura boneti" "Isthmura corrugata"
## [243] "Isthmura gigantea" "Isthmura maxima"
## [245] "Isthmura naucampatepetl" "Isthmura sierraoccidentalis"
## [247] "Ixalotriton niger" "Ixalotriton parvus"
## [249] "Nototriton abscondens" "Nototriton barbouri"
## [251] "Nototriton brodiei" "Nototriton costaricense"
## [253] "Nototriton gamezi" "Nototriton guanacaste"
## [255] "Nototriton lignicola" "Nototriton limnospectator"
## [257] "Nototriton major" "Nototriton matama"
## [259] "Nototriton mime" "Nototriton nelsoni"
## [261] "Nototriton oreadorum" "Nototriton picadoi"
## [263] "Nototriton picucha" "Nototriton richardi"
## [265] "Nototriton saslaya" "Nototriton stuarti"
## [267] "Nototriton tapanti" "Nototriton tomamorum"
## [269] "Nyctanolis pernix" "Oedipina alfaroi"
## [271] "Oedipina alleni" "Oedipina altura"
## [273] "Oedipina berlini" "Oedipina capitalina"
## [275] "Oedipina carablanca" "Oedipina chortiorum"
## [277] "Oedipina collaris" "Oedipina complex"
## [279] "Oedipina cyclocauda" "Oedipina ecuatoriana"
## [281] "Oedipina elongata" "Oedipina fortunensis"
## [283] "Oedipina gephyra" "Oedipina gracilis"
## [285] "Oedipina grandis" "Oedipina ignea"
## [287] "Oedipina kasios" "Oedipina koehleri"
## [289] "Oedipina leptopoda" "Oedipina maritima"
## [291] "Oedipina motaguae" "Oedipina nica"
## [293] "Oedipina nimaso" "Oedipina pacificensis"
## [295] "Oedipina parvipes" "Oedipina paucidentata"
## [297] "Oedipina petiola" "Oedipina poelzi"
## [299] "Oedipina pseudouniformis" "Oedipina quadra"
## [301] "Oedipina salvadorensis" "Oedipina savagei"
## [303] "Oedipina stenopodia" "Oedipina stuarti"
## [305] "Oedipina taylori" "Oedipina tomasi"
## [307] "Oedipina tzutujilorum" "Oedipina uniformis"
## [309] "Oedipina villamizariorum" "Parvimolge townsendi"
## [311] "Pseudoeurycea ahuitzotl" "Pseudoeurycea altamontana"
## [313] "Pseudoeurycea amuzga" "Pseudoeurycea anitae"
## [315] "Pseudoeurycea aquatica" "Pseudoeurycea aurantia"
## [317] "Pseudoeurycea brunnata" "Pseudoeurycea cochranae"
## [319] "Pseudoeurycea conanti" "Pseudoeurycea exspectata"
## [321] "Pseudoeurycea firscheini" "Pseudoeurycea gadovii"
## [323] "Pseudoeurycea goebeli" "Pseudoeurycea granitum"
## [325] "Pseudoeurycea juarezi" "Pseudoeurycea kuautli"
## [327] "Pseudoeurycea leprosa" "Pseudoeurycea lineola"
## [329] "Pseudoeurycea longicauda" "Pseudoeurycea lynchi"
## [331] "Pseudoeurycea melanomolga" "Pseudoeurycea mixcoatl"
## [333] "Pseudoeurycea mixteca" "Pseudoeurycea mystax"
## [335] "Pseudoeurycea nigromaculata" "Pseudoeurycea obesa"
## [337] "Pseudoeurycea orchileucos" "Pseudoeurycea orchimelas"
## [339] "Pseudoeurycea papenfussi" "Pseudoeurycea rex"
## [341] "Pseudoeurycea robertsi" "Pseudoeurycea ruficauda"
## [343] "Pseudoeurycea saltator" "Pseudoeurycea smithi"
## [345] "Pseudoeurycea tenchalli" "Pseudoeurycea teotepec"
## [347] "Pseudoeurycea tlahcuiloh" "Pseudoeurycea tlilicxitl"
## [349] "Pseudoeurycea unguidentis" "Pseudoeurycea werleri"
## [351] "Pseudotriton diastictus" "Pseudotriton montanus"
## [353] "Pseudotriton ruber" "Stereochilus marginatus"
## [355] "Thorius adelos" "Thorius arboreus"
## [357] "Thorius aureus" "Thorius boreas"
## [359] "Thorius dubitus" "Thorius grandis"
## [361] "Thorius hankeni" "Thorius infernalis"
## [363] "Thorius insperatus" "Thorius longicaudus"
## [365] "Thorius lunaris" "Thorius macdougalli"
## [367] "Thorius magnipes" "Thorius maxillabrochus"
## [369] "Thorius minutissimus" "Thorius minydemus"
## [371] "Thorius munificus" "Thorius narismagnus"
## [373] "Thorius narisovalis" "Thorius omiltemi"
## [375] "Thorius papaloae" "Thorius pennatulus"
## [377] "Thorius pinicola" "Thorius pulmonaris"
## [379] "Thorius schmidti" "Thorius smithi"
## [381] "Thorius spilogaster" "Thorius tlaxiacus"
## [383] "Thorius troglodytes" "Urspelerpes brucei"
## [385] "Aneides aeneus" "Aneides caryaensis"
## [387] "Aneides ferreus" "Aneides flavipunctatus"
## [389] "Aneides hardii" "Aneides iecanus"
## [391] "Aneides klamathensis" "Aneides lugubris"
## [393] "Aneides niger" "Aneides vagrans"
## [395] "Desmognathus abditus" "Desmognathus aeneus"
## [397] "Desmognathus apalachicolae" "Desmognathus aureatus"
## [399] "Desmognathus auriculatus" "Desmognathus brimleyorum"
## [401] "Desmognathus carolinensis" "Desmognathus conanti"
## [403] "Desmognathus folkertsi" "Desmognathus fuscus"
## [405] "Desmognathus imitator" "Desmognathus marmoratus"
## [407] "Desmognathus melanius" "Desmognathus monticola"
## [409] "Desmognathus ochrophaeus" "Desmognathus ocoee"
## [411] "Desmognathus orestes" "Desmognathus organi"
## [413] "Desmognathus planiceps" "Desmognathus quadramaculatus"
## [415] "Desmognathus santeetlah" "Desmognathus valentinei"
## [417] "Desmognathus welteri" "Desmognathus wrighti"
## [419] "Ensatina eschscholtzii" "Hydromantes brunus"
## [421] "Hydromantes platycephalus" "Hydromantes samweli"
## [423] "Hydromantes shastae" "Hydromantes wintu"
## [425] "Karsenia koreana" "Phaeognathus hubrichti"
## [427] "Plethodon ainsworthi" "Plethodon albagula"
## [429] "Plethodon amplus" "Plethodon angusticlavius"
## [431] "Plethodon asupak" "Plethodon aureolus"
## [433] "Plethodon caddoensis" "Plethodon chattahoochee"
## [435] "Plethodon cheoah" "Plethodon chlorobryonis"
## [437] "Plethodon cinereus" "Plethodon cylindraceus"
## [439] "Plethodon dixi" "Plethodon dorsalis"
## [441] "Plethodon dunni" "Plethodon electromorphus"
## [443] "Plethodon elongatus" "Plethodon fourchensis"
## [445] "Plethodon glutinosus" "Plethodon hoffmani"
## [447] "Plethodon hubrichti" "Plethodon idahoensis"
## [449] "Plethodon jacksoni" "Plethodon jordani"
## [451] "Plethodon kentucki" "Plethodon kiamichi"
## [453] "Plethodon kisatchie" "Plethodon larselli"
## [455] "Plethodon meridianus" "Plethodon metcalfi"
## [457] "Plethodon montanus" "Plethodon neomexicanus"
## [459] "Plethodon nettingi" "Plethodon ocmulgee"
## [461] "Plethodon ouachitae" "Plethodon pauleyi"
## [463] "Plethodon petraeus" "Plethodon punctatus"
## [465] "Plethodon richmondi" "Plethodon savannah"
## [467] "Plethodon sequoyah" "Plethodon serratus"
## [469] "Plethodon shenandoah" "Plethodon sherando"
## [471] "Plethodon shermani" "Plethodon stormi"
## [473] "Plethodon teyahalee" "Plethodon vandykei"
## [475] "Plethodon variolatus" "Plethodon vehiculum"
## [477] "Plethodon ventralis" "Plethodon virginia"
## [479] "Plethodon websteri" "Plethodon wehrlei"
## [481] "Plethodon welleri" "Plethodon yonahlossee"
## [483] "Speleomantes ambrosii" "Speleomantes flavus"
## [485] "Speleomantes genei" "Speleomantes imperialis"
## [487] "Speleomantes italicus" "Speleomantes sarrabusensis"
## [489] "Speleomantes strinatii" "Speleomantes supramontis"plethodontid.stats<-aswStats(asw_taxonomy, Family = "Plethodontidae",verbose = T)
par(mar=c(1,1,1,1))
pie(plethodontid.stats$Genera[order(plethodontid.stats$Genera, decreasing = T)], cex=0.5, main = "No. of Species per Genus", col = rainbow(length(plethodontid.stats$Genera),s = 0.5), clockwise = T, border = NA)