Skip to content

dlizcano/mammalcol

Repository files navigation

mammalcol

R-CMD-check Codecov test coverage CRAN status lifecycle size

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")

load library

library(mammalcol)
#> This is mammalcol 0.2.3
#> 
#> Attaching package: 'mammalcol'
#> The following objects are masked _by_ '.GlobalEnv':
#> 
#>     mammalmap, search_mammalcol, sp_by_depto

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       17

Search 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       12

Produce 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:3535811

Search 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 | Tolima

The 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 Santander

The 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 | Tolima

Sugested 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