R/search_mammalcol.R
search_mammalcol.RdThis function takes a list of Mammal species names, searches for their data in the MammalCol pacakage dataset, and returns a data frame containing the relevant information for each species.
search_mammalcol(splist, max_distance = 0.2)A data frame containing the retrieved information for each species.
The function allows fuzzy matching for species names with a maximum distance threshold to handle potential typos or variations in species names.
library(mammalcol)
splist <- c("Tapirus bairdii", "Tapirus pinchaque", "Tapirus terrestris",
"Tapirus terrestris", "tapir terrestre", "Pudu mephistophiles")
search_mammalcol(splist)
#> The following names are repeated in the 'splist': Tapirus terrestris
#> name_submitted
#> 1 Tapirus bairdii
#> 2 Tapirus pinchaque
#> 3 Tapirus terrestris
#> 5 Pudu mephistophiles
#> taxonID
#> 1 gbif.org/species/2440897
#> 2 urn:lsid:catalogueoflife.org:taxon:4f2010e3-5e17-11e7-8cee-bc764e092680:col20170824
#> 3 urn:lsid:catalogueoflife.org:taxon:4f200f4b-5e17-11e7-8cee-bc764e092680:col20170824
#> 5 urn:lsid:catalogueoflife.org:taxon:4f167916-5e17-11e7-8cee-bc764e092680:col20170824
#> scientificNameID
#> 1 https://www.gbif.org/species/2440897
#> 2 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=624999
#> 3 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=625000
#> 5 http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=625074
#> scientificName
#> 1 Tapirus bairdii
#> 2 Tapirus pinchaque
#> 3 Tapirus terrestris
#> 5 Pudella mephistophiles
#> nameAccordingTo
#> 1 Tapirus bairdii (Gill, 1865) in GBIF Secretariat (2017). GBIF Backbone Taxonomy. Checklist dataset https://doi.org/10.15468/39omei accessed via GBIF.org on 2019-08-01.
#> 2 Tom Orrell (custodian), Dave Nicolson (ed). (2019). ITIS Global: The Integrated Taxonomic Information System (version Jun 2017). In: Species 2000 & ITIS Catalogue of Life, 2019 Annual Checklist (Roskov Y., Ower G., Orrell T., Nicolson D., Bailly N., Kirk P.M., Bourgoin T., DeWalt R.E., Decock W., Nieukerken E. van, Zarucchi J., Penev L., eds.). Digital resource at www.catalogueoflife.org/annual-checklist/2019. Species 2000: Naturalis, Leiden, the Netherlands. ISSN 2405-884X.
#> 3 Tom Orrell (custodian), Dave Nicolson (ed). (2019). ITIS Global: The Integrated Taxonomic Information System (version Jun 2017). In: Species 2000 & ITIS Catalogue of Life, 2019 Annual Checklist (Roskov Y., Ower G., Orrell T., Nicolson D., Bailly N., Kirk P.M., Bourgoin T., DeWalt R.E., Decock W., Nieukerken E. van, Zarucchi J., Penev L., eds.). Digital resource at www.catalogueoflife.org/annual-checklist/2019. Species 2000: Naturalis, Leiden, the Netherlands. ISSN 2405-884X.
#> 5 Barrio, J., Gutiérrez, E.E. and D'Elía, G. 2024-03-01. The first living cervid species described in the 21st century and revalidation of Pudella (Artiodactyla). Journal of Mammalogy 105(3):577-588.
#> kingdom phylum class order family genus specificEpithet
#> 1 Animalia Chordata Mammalia Perissodactyla Tapiridae Tapirus bairdii
#> 2 Animalia Chordata Mammalia Perissodactyla Tapiridae Tapirus pinchaque
#> 3 Animalia Chordata Mammalia Perissodactyla Tapiridae Tapirus terrestris
#> 5 Animalia Chordata Mammalia Artiodactyla Cervidae Pudella mephistophiles
#> taxonRank scientificNameAuthorship taxonomicStatus taxonRemarks
#> 1 Especie (Gill, 1865) Válido Elevación (m): 0-1000
#> 2 Especie (Roulin, 1829) Válido Elevación (m): 1400-4000
#> 3 Especie (Linnaeus, 1758) Válido Elevación (m): 0-2400
#> 5 Especie (de Winton, 1896) Válido Elevación (m): 3000-3500
#> language rightsHolder
#> 1 es Sociedad Colombiana de Mastozoología
#> 2 es Sociedad Colombiana de Mastozoología
#> 3 es Sociedad Colombiana de Mastozoología
#> 5 es Sociedad Colombiana de Mastozoología
#> bibliographicCitation
#> 1 HERSHKOVITZ P. 1954. Mammals of northern Colombia. Preliminary report No. 7: Tapirs (genus Tapirus), with a systematic review of American species. Proceedings of the United States National Museum 103:465-496.
#> 2 ARIAS-ALZATE A, CC DOWNER, C DELGADO-V y J SÁNCHEZ-LONDOÑO. 2010. Un registro de tapir de montaña (Tapirus pinchaque) en el norte de la Cordillera Occidental de Colombia. Mastozoología Neotropical 17:111-116.
#> 3 ARIAS-ALZATE A, JA PALACIO VIEIRA y J MUÑOZ-DURAN. 2009. Nuevos registros de distribución y oferta de hábitat de la danta colombiana (Tapirus terrestris colombianus) en las tierras bajas del norte de la Cordillera Central (Colombia). Mastozoología Neotropical 16:19-25.
#> 5 ALBERICO M, A CADENA, JI HERNÁNDEZ-CAMACHO y Y MUÑOZ-SABA. 2000b. Mamíferos (Synapsida: Theria) de Colombia. Biota Colombiana 1:43-75.
#> inMDD Col_redlist
#> 1 1 EN A2cd+ B1ab (i,ii,iii)+ B2ab (i, ii, iii)
#> 2 1 EN A4cd
#> 3 1 VU A4cd
#> 5 0 <NA>
#> distribution
#> 1 Antioquia | Chocó | Córdoba
#> 2 Antioquia | Cauca | Cundinamarca | Huila | Meta | Nariño | Quindío | Risaralda | Tolima | Valle del Cauca | Caldas | Caquetá | Putumayo
#> 3 Antioquia | Amazonas | Arauca | Caquetá | Cauca | Cesar | Córdoba | Guainía | La Guajira | Meta | Magdalena | Vaupés | Vichada | Guaviare | Casanare | Norte de Santander | Putumayo
#> 5 Cauca | Huila | Nariño | Risaralda | Quindío | Tolima | Valle del Cauca
#> endemic english_name Distance
#> 1 No Central American Tapir 21
#> 2 No Mountain Tapir 77
#> 3 No Lowland Tapir 78
#> 5 No <NA> 77