README.md

In sckott/spplist: Get Species Lists from Many Data Sources

spplist

spplist = get you some species lists

here's how i'm thinking about the workflow:

• search, retrieve list
• parse to certain rank (limited to spp vs genus)
• clean names - capitalization, etc.
• write to csv/etc.

Thoughts?

Installation

remotes::install_github("sckott/spplist")

library("spplist")

Get a spp list from iDigBio

via the spocc package

geometry <- "POLYGON((8.98 48.05,15.66 48.05,15.66 45.40,8.98 45.40,8.98 48.05))"
spp_list(geometry = geometry, from = "idigbio", limit = 20)

## <Species list>
## No. Returned: 19
##   idigbio: 19

Get a list from many sources

geometry <- "POLYGON((8.98 48.05,15.66 48.05,15.66 45.40,8.98 45.40,8.98 48.05))"
spp_list(geometry = geometry, from = c("idigbio", "inat"), limit = 20)

## <Species list>
## No. Returned: 36
##   idigbio: 19
##   inat: 17

note how the limit parameter doesn't necessarily give you the number you request. Rather, that number is the max occurrence records pulled down, and there could be duplicate names.

Get species lists from GBIF

using rgbif

Search by geometry

geometry <- "POLYGON((8.98 48.05,15.66 48.05,15.66 45.40,8.98 45.40,8.98 48.05))"
spp_list_gbif(geometry = geometry, limit = 20)

## [1] "Aythya fuligula (Linnaeus, 1758)"    "Columba palumbus Linnaeus, 1758"    
## [3] "Erithacus rubecula (Linnaeus, 1758)" "Fringilla coelebs Linnaeus, 1758"   
## [5] "Mahonia aquifolium (Pursh) Nutt."    "Phyllostachys Siebold & Zucc."      
## [7] "Podarcis muralis (Laurenti, 1768)"   "Prunus laurocerasus L."             
## [9] "Rhus typhina L."

Search by country

(res <- spp_list_gbif(country = 'US', limit = 20))

##  [1] "Acanthurus coeruleus Bloch & Schneider, 1801"   
##  [2] "Agelaius phoeniceus (Linnaeus, 1766)"           
##  [3] "Allium triquetrum L."                           
##  [4] "Cairina moschata (Linnaeus, 1758)"              
##  [5] "Catharus guttatus (Pallas, 1811)"               
##  [6] "Dryobates pubescens (Linnaeus, 1766)"           
##  [7] "Falco mexicanus Schlegel, 1850"                 
##  [8] "Haemorhous mexicanus (P.L.Statius Müller, 1776)"
##  [9] "Ilex vomitoria Aiton"                           
## [10] "Leucophaeus atricilla (Linnaeus, 1758)"         
## [11] "Liquidambar styraciflua L."                     
## [12] "Lontra canadensis (Schreber, 1777)"             
## [13] "Lophodytes cucullatus (Linnaeus, 1758)"         
## [14] "Melospiza melodia (A.Wilson, 1810)"             
## [15] "Morella cerifera Small"                         
## [16] "Panicum virgatum L."                            
## [17] "Phalacrocorax auritus (Lesson, 1831)"           
## [18] "Selaginella galeottii Spring"                   
## [19] "Spinus pinus (A.Wilson, 1810)"

Meta

• Please report any issues or bugs.
• License: MIT
• Get citation information for spplist in R doing citation(package = 'spplist')
• Please note that the spplist project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

sckott/spplist documentation built on Dec. 1, 2020, 5:30 p.m.