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

install.packages("devtools")
devtools::install_github("ropenscilabs/spplist")
library("spplist")

Get a spp list from iDigBio

via the spocc package

## $idigbio
##  [1] "agonum viduum"                          
##  [2] "anthidiellum (ananthidiellum) strigatum"
##  [3] "bembidion articulatum"                  
##  [4] "cardamine amara"                        
##  [5] "clitocybe geotropa"                     
##  [6] "collema auriforme"                      
##  [7] "cortinarius subtortus"                  
##  [8] "dicentrarchus labrax"                   
##  [9] "graptodytes granularis"                 
## [10] "lecanora mughicola"                     
## [11] "lecidea turgidula"                      
## [12] "microtus subterraneus incertoides"      
## [13] "mus musculus domesticus"                
## [14] "ochrolechia alboflavescens"             
## [15] "philonthus carbonarius"                 
## [16] "physconia perisidiosa"                  
## [17] "rhizocarpon kakurgon"                   
## [18] "rhodymenia ligulata"                    
## [19] "zeus faber"

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)
## $idigbio
##  [1] "agonum viduum"                          
##  [2] "anthidiellum (ananthidiellum) strigatum"
##  [3] "bembidion articulatum"                  
##  [4] "cardamine amara"                        
##  [5] "clitocybe geotropa"                     
##  [6] "collema auriforme"                      
##  [7] "cortinarius subtortus"                  
##  [8] "dicentrarchus labrax"                   
##  [9] "graptodytes granularis"                 
## [10] "lecanora mughicola"                     
## [11] "lecidea turgidula"                      
## [12] "microtus subterraneus incertoides"      
## [13] "mus musculus domesticus"                
## [14] "ochrolechia alboflavescens"             
## [15] "philonthus carbonarius"                 
## [16] "physconia perisidiosa"                  
## [17] "rhizocarpon kakurgon"                   
## [18] "rhodymenia ligulata"                    
## [19] "zeus faber"                             
## 
## $inat
##  [1] "Ajuga pyramidalis"           "Asarum europaeum europaeum" 
##  [3] "Buteo buteo"                 "Cryptocephalus sericeus"    
##  [5] "Dasyphora albofasciata"      "Exorista rustica"           
##  [7] "Lacerta bilineata bilineata" "Lacerta viridis viridis"    
##  [9] "Meromyza femorata"           "Morus alba"                 
## [11] "Populus nigra"               "Populus x canescens"        
## [13] "Primula vulgaris"            "Pyrausta despicata"         
## [15] "Salix elaeagnos"             "Sciurus vulgaris"

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

##  [1] "Anas platyrhynchos"    "Anser anser"          
##  [3] "Ardea cinerea"         "Aythya ferina"        
##  [5] "Aythya fuligula"       "Buteo buteo"          
##  [7] "Cinclus cinclus"       "Corvus corone"        
##  [9] "Cyclamen purpurascens" "Fulica atra"          
## [11] "Hedera helix"          "Mergus merganser"     
## [13] "Netta rufina"          "Phalacrocorax carbo"  
## [15] "Podiceps cristatus"    "Primula vulgaris"     
## [17] "Rubus laciniatus"      "Salamandra salamandra"
## [19] "Spinus spinus"

Search by country

(res <- spp_list_gbif(country = 'US', limit = 20))
##  [1] "Acer rubrum"           "Aureoboletus"         
##  [3] "Buteo jamaicensis"     "Calycopis cecrops"    
##  [5] "Cathartes aura"        "Centaurea melitensis" 
##  [7] "Cryptochiton stelleri" "Fagus grandifolia"    
##  [9] "Homo sapiens"          "Marasmius plicatulus" 
## [11] "Melospiza melodia"     "Mephitis mephitis"    
## [13] "Mycena maculata"       "Pipilo maculatus"     
## [15] "Regulus calendula"     "Sayornis saya"        
## [17] "Sciurus carolinensis"  "Strix varia"          
## [19] "Tamias striatus"

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