The goal of mammalcol is to allow easy access to the List of Mammal Species of Colombia.
Researchers can explore Colombia’s amazing variety of mammals using the mammalcol R package. This package includes information on 548 mammal species, making Colombia one of the world leaders in mammal diversity. The data comes from the latest “Checklist of the mammals (Mammalia) of Colombia” by Ramírez-Chaves et al (2021). But It’s important to remember that how scientists classify mammals keeps changing constantly, so the information in this package has been updated with the checklist Mamíferos de Colombia, which is published and updated regularly by the Colombian Mammal Society.
Installation
You can install the development version of mammalcol from GitHub with:
# install.packages("devtools")
devtools::install_github("dlizcano/mammalcol")Example
Search database
This is a basic example which shows you how to search mammal names in Colombia using a vector of mammal names.
# define a vector with species to search for
splist <- c("Tapirus bairdii", "Tapirus pinchaque", "Tapirus terrestris",
"Tapirus terrestris", "Pudu mephistophiles", "Tapirus bairdii")
# search in database
search_mammalcol(splist)
#> The following names are repeated in the 'splist': Tapirus bairdii, Tapirus terrestris
#> name_submitted kingdom phylum class order family
#> 1 Tapirus bairdii Animalia Chordata Mammalia Perissodactyla Tapiridae
#> 2 Tapirus pinchaque Animalia Chordata Mammalia Perissodactyla Tapiridae
#> 3 Tapirus terrestris Animalia Chordata Mammalia Perissodactyla Tapiridae
#> 4 Pudu mephistophiles Animalia Chordata Mammalia Artiodactyla Cervidae
#> genus specificEpithet taxonRank scientificNameAuthorship
#> 1 Tapirus bairdii Especie (Gill, 1865)
#> 2 Tapirus pinchaque Especie (Roulin, 1829)
#> 3 Tapirus terrestris Especie (Linnaeus, 1758)
#> 4 Pudu mephistophiles Especie (de Winton, 1896)
#> taxonRemarks
#> 1 Elevación (m): 0-1000
#> 2 Elevación (m): 1400-4000
#> 3 Elevación (m): 0-2400
#> 4 Elevación (m): 3000-3500
#> 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.
#> 4 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
#> 4 1 EN A2cd B1ab (i; ii; iii; iv; v) \r\n
#> 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
#> 4 Cauca | Huila | Nariño | Risaralda | Quindío | Tolima | Valle del Cauca
#> source endemic
#> 1 Proceedings of the United States National Museum 103:465-496 No
#> 2 Mastozoología Neotropical 17:111-116 No
#> 3 Mastozoología Neotropical 16:19-25 No
#> 4 Biota Colombiana 1:43-75 No
#> english_name
#> 1 Central American Tapir
#> 2 Mountain Tapir
#> 3 Lowland Tapir
#> 4 Northern Pudu
#> id
#> 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
#> 4 urn:lsid:catalogueoflife.org:taxon:4f167916-5e17-11e7-8cee-bc764e092680:col20170824
#> Distance
#> 1 12
#> 2 14
#> 3 16
#> 4 17Search database with typos
mammalcol has the ability to identify and correct minor typos and lower case in the genus. Correcting potential typos or variations in species names through fuzzy matching is a crucial aspect of data management. This technique ensures precise retrieval by adeptly identifying and accommodating minor differences in input names, thus enhancing the reliability of analyses conducted on diverse, inconsistent, and ensemble datasets.
# vector with species names and intentional typos
splist <- c("Tapiru terrestre", "pudu mephistophiles", "tapirus bairdii")
# search in database
search_mammalcol(splist)
#> name_submitted kingdom phylum class order family
#> 1 Tapiru terrestre Animalia Chordata Mammalia Perissodactyla Tapiridae
#> 2 Pudu mephistophiles Animalia Chordata Mammalia Artiodactyla Cervidae
#> 3 Tapirus bairdii Animalia Chordata Mammalia Perissodactyla Tapiridae
#> genus specificEpithet taxonRank scientificNameAuthorship
#> 1 Tapirus terrestris Especie (Linnaeus, 1758)
#> 2 Pudu mephistophiles Especie (de Winton, 1896)
#> 3 Tapirus bairdii Especie (Gill, 1865)
#> taxonRemarks
#> 1 Elevación (m): 0-2400
#> 2 Elevación (m): 3000-3500
#> 3 Elevación (m): 0-1000
#> bibliographicCitation
#> 1 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.
#> 2 ALBERICO M, A CADENA, JI HERNÁNDEZ-CAMACHO y Y MUÑOZ-SABA. 2000b. Mamíferos (Synapsida: Theria) de Colombia. Biota Colombiana 1:43-75.
#> 3 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.
#> inMDD Col_redlist
#> 1 1 VU A4cd
#> 2 1 EN A2cd B1ab (i; ii; iii; iv; v) \r\n
#> 3 1 EN A2cd+ B1ab (i,ii,iii)+ B2ab (i, ii, iii)
#> distribution
#> 1 Antioquia | Amazonas | Arauca | Caquetá | Cauca | Cesar | Córdoba | Guainía | La Guajira | Meta | Magdalena | Vaupés | Vichada | Guaviare | Casanare | Norte de Santander | Putumayo
#> 2 Cauca | Huila | Nariño | Risaralda | Quindío | Tolima | Valle del Cauca
#> 3 Antioquia | Chocó | Córdoba
#> source endemic
#> 1 Mastozoología Neotropical 16:19-25 No
#> 2 Biota Colombiana 1:43-75 No
#> 3 Proceedings of the United States National Museum 103:465-496 No
#> english_name
#> 1 Lowland Tapir
#> 2 Northern Pudu
#> 3 Central American Tapir
#> id
#> 1 urn:lsid:catalogueoflife.org:taxon:4f200f4b-5e17-11e7-8cee-bc764e092680:col20170824
#> 2 urn:lsid:catalogueoflife.org:taxon:4f167916-5e17-11e7-8cee-bc764e092680:col20170824
#> 3 gbif.org/species/2440897
#> Distance
#> 1 15
#> 2 17
#> 3 12Produce a map
The function mammalmap produces basic a map of distribution at the “Departamento” level for a single species.
# write a species name in the function to map it
mammalmap("Tapirus pinchaque")
Remove the legeng
Using the parameter legend=FALSE
# write a species name in the function to map it
mammalmap("Tapirus pinchaque", legend=FALSE)
See the full taxon table
head(taxon)
#> scientificName kingdom phylum class order family
#> 1 Passalites murelia Animalia Chordata Mammalia Artiodactyla Cervidae
#> 2 Mazama rufina Animalia Chordata Mammalia Artiodactyla Cervidae
#> 3 Passalites sanctaemartae Animalia Chordata Mammalia Artiodactyla Cervidae
#> 4 Mazama temama Animalia Chordata Mammalia Artiodactyla Cervidae
#> 5 Mazama zamora Animalia Chordata Mammalia Artiodactyla Cervidae
#> 6 Mazama zetta Animalia Chordata Mammalia Artiodactyla Cervidae
#> genus specificEpithet taxonRank scientificNameAuthorship
#> 1 Passalites murelia Especie J. A. Allen, 1915
#> 2 Mazama rufina Especie (Pucheran, 1851)
#> 3 Passalites sanctaemartae Especie (J. A. Allen, 1915)
#> 4 Mazama temama Especie (Kerr, 1792)
#> 5 Mazama zamora Especie J. A. Allen, 1915
#> 6 Mazama zetta Especie Thomas, 1913
#> taxonRemarks
#> 1 Elevación (m): 0-900
#> 2 Elevación (m): 1500-4000
#> 3 Elevación (m): 0-900
#> 4 Elevación (m): 0-68
#> 5 Elevación (m): 600-1200
#> 6 Elevación (m): 1600-1950
#> bibliographicCitation
#> 1 ALLEN JA. 1916. List of mammals collected in Colombia by the American Museum of Natural History expeditions, 1910-1915. Bulletin of the American Museum of Natural History 35:191-238.
#> 2 ALBERICO M, A CADENA, JI HERNÁNDEZ-CAMACHO y Y MUÑOZ-SABA. 2000b. Mamíferos (Synapsida: Theria) de Colombia. Biota Colombiana 1:43-75.
#> 3 ALLEN JA. 1916. List of mammals collected in Colombia by the American Museum of Natural History expeditions, 1910-1915. Bulletin of the American Museum of Natural History 35:191-238.
#> 4 GROVES C y P GRUBB. 1987. Relationships of living deer. Pp. 21-59, en: Biology and management of the Cervidae (CM Wemmer, ed.). Smithsonian Institution Press, Washington, D.C., USA.
#> 5 ALLEN JA. 1916. List of mammals collected in Colombia by the American Museum of Natural History expeditions, 1910-1915. Bulletin of the American Museum of Natural History 35:191-238.
#> 6 ALLEN JA. 1916. List of mammals collected in Colombia by the American Museum of Natural History expeditions, 1910-1915. Bulletin of the American Museum of Natural History 35:191-238.
#> inMDD Col_redlist
#> 1 0 <NA>
#> 2 1 VU A2 cde\r\n
#> 3 0 <NA>
#> 4 1 DD
#> 5 0 DD
#> 6 0 DD
#> distribution
#> 1 Amazonas | Caquetá | Cauca | Meta | Vaupés | Vichada | Nariño | Putumayo | Cundinamarca
#> 2 Antioquia | Boyacá | Caldas | Cauca | Cesar | Cundinamarca | Huila | Nariño | Norte de Santander | Quindío | Risaralda | Santander | Tolima | Valle del Cauca | Caquetá
#> 3 Bolívar | Cesar | La Guajira | Magdalena | Atlántico | Córdoba | Cundinamarca
#> 4 Chocó | Magdalena
#> 5 Amazonas | Caquetá | Meta | Putumayo | Vichada
#> 6 Antioquia | Caldas | Cauca | Nariño | Valle del Cauca | Tolima
#> source
#> 1 Bulletin of the American Museum of Natural History 35:191-238
#> 2 Biota Colombiana 1:43-75
#> 3 Bulletin of the American Museum of Natural History 35:191-238
#> 4 Pp. 21-59, en: Biology and management of the Cervidae (CM Wemmer, ed.). Smithsonian Institution Press, Washington, D.C., USA
#> 5 Bulletin of the American Museum of Natural History 35:191-238
#> 6 Bulletin of the American Museum of Natural History 35:191-238
#> endemic english_name
#> 1 No <NA>
#> 2 No Little Red Brocket
#> 3 No <NA>
#> 4 No Mexican Red Brocket
#> 5 No <NA>
#> 6 No <NA>
#> id
#> 1 urn:lsid:organismnames.com:name:3484299
#> 2 urn:lsid:catalogueoflife.org:taxon:4f16759f-5e17-11e7-8cee-bc764e092680:col20170824
#> 3 eol.org/pages/Mazama%20sanctaemartae
#> 4 urn:lsid:catalogueoflife.org:taxon:259114ac-5e17-11e7-8cee-bc764e092680:col20170824
#> 5 urn:lsid:organismnames.com:name:3484302
#> 6 urn:lsid:organismnames.com:name:3535811Search mammals present by departamento
Use the departamento name or a vector of departamentos to know the mammals species present. The argument type = “any” retrieve mammals present in any of those departamentos.
occ.any <- sp_by_depto(c("Arauca", "Norte de Santander"), type = "any")
head(occ.any)
#> scientificName family order
#> 1 Vampyressa voragine Phyllostomidae Chiroptera
#> 2 Odocoileus goudotii Cervidae Artiodactyla
#> 3 Chilomys fumeus Cricetidae Rodentia
#> 4 Melanomys columbianus Cricetidae Rodentia
#> 5 Tonatia maresi Phyllostomidae Chiroptera
#> 6 Coendou pruinosus Erethizontidae Rodentia
#> locality
#> 1 Casanare | Norte de Santander
#> 2 Boyacá | Cundinamarca | Santander | Norte de Santander
#> 3 Norte de Santander
#> 4 Magdalena | Norte de Santander
#> 5 Amazonas | Caquetá | Casanare | Huila | Meta | Putumayo | Vaupés | Guaviare | Arauca | Guainía
#> 6 Cundinamarca | Norte de Santander | Santander | Guainía | Meta | Arauca | TolimaThe argument type = “only” retrieves species present only in that departamento and in no other departamento.
occ.only <- sp_by_depto(c("Norte de Santander"), type = "only")
head(occ.only)
#> scientificName family order locality
#> 1 Chilomys fumeus Cricetidae Rodentia Norte de SantanderThe argument all retrieves species present in both departamentos. The argument taxa limit the search to one order. occ.bats has the bats present in Arauca and Norte de Santander.
occ.all <- sp_by_depto(c("Arauca", "Norte de Santander"), type = "all")
occ.bats <- sp_by_depto(c("Arauca", "Norte de Santander"), type = "all", taxa = "Chiroptera")
head(occ.bats)
#> scientificName family order
#> 1 Dermanura phaeotis Phyllostomidae Chiroptera
#> 2 Molossus rufus Molossidae Chiroptera
#> 3 Cynomops planirostris Molossidae Chiroptera
#> 4 Vampyressa thyone Phyllostomidae Chiroptera
#> 5 Enchisthenes hartii Phyllostomidae Chiroptera
#> 6 Micronycteris microtis Phyllostomidae Chiroptera
#> locality
#> 1 Antioquia | Cauca | Chocó | Nariño | Quindío | Risaralda | Valle del Cauca | Amazonas | Arauca | Caldas | Caquetá | Córdoba | Guainía | Magdalena | Norte de Santander | Putumayo | Santander | Tolima
#> 2 Arauca | Caldas | Norte de Santander | Tolima | Putumayo | Guaviare | Amazonas | Antioquia | Atlántico | Caquetá | Casanare | Guainía | Meta | Vichada
#> 3 Amazonas | Arauca | Boyacá | Casanare | Meta | Vichada | Caquetá | Cundinamarca | Norte de Santander | Putumayo | Guainía | Sucre
#> 4 Caldas | Cauca | Quindío | Risaralda | Amazonas | Caquetá | Guaviare | Meta | Putumayo | Antioquia | Arauca | Casanare | Chocó | Córdoba | Guainía | Magdalena | Nariño | Norte de Santander | Sucre | Tolima | Valle del Cauca | Vaupés | Vichada
#> 5 Caldas | Cauca | Cundinamarca | Quindío | Risaralda | Amazonas | Caquetá | Putumayo | Antioquia | Arauca | Casanare | Cesar | Chocó | Guainía | Huila | Magdalena | Nariño | Norte de Santander | Putumayo | Tolima | Valle del Cauca
#> 6 Cundinamarca | Magdalena | Amazonas | Caquetá | Guaviare | Arauca | Casanare | Chocó | Córdoba | Guainía | Norte de Santander | TolimaSugested citation
citation("mammalcol")
#> To cite mammalcol package in publications use:
#>
#> Lizcano, DJ. et al., (2024). mammalcol: Access to the List of Mammal
#> Species of Colombia. R package version 0.2.2
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {mammalcol: Access to the List of Mammal Species of Colombia},
#> author = {Diego J. Lizcano and Baltazar González and Alejandra Bonilla-Sánchez and Andres F. Suárez-Castro and Camilo A. Calderón-Acevedo},
#> year = {2024},
#> note = {R data package version 0.2.2},
#> url = {https://dlizcano.github.io/mammalcol/},
#> }
#>
#> To cite just the original mammalcol dataset, please use: Mammals of
#> Colombia / Mamíferos de Colombia. SCMas: <doi:10.15472/kl1whs>, but
#> keep in mind taxonomy is dinamic and have changed.Lizcano, DJ. (2024). mammalcol: Access to the List of Mammal Species of Colombia. R package version 0.1.0
