In ropenscilabs/spplit: Combine Species Occurrence Data and Literature

Get metadata on CAS datasets from different occurrence data providers

setup

library("dplyr")
library("rgbif")

Dataset keys for CAS

GBIF

x <- rgbif::datasets(query = "CAS")
dat <- x$data[grep("^CAS", x$data$title), ]

the keys

dat$key
#> [1] "6ce7290f-47f6-4046-8356-371f5b6749df"
#> [2] "4f29b6ab-20c0-4479-8795-4915bedcebd1"
#> [3] "f934f8e2-32ca-46a7-b2f8-b032a4740454"
#> [4] "5d6c10bd-ea31-4363-8b79-58c96d859f5b"
#> [5] "14f3151a-e95d-493c-a40d-d9938ef62954"
#> [6] "44bcde48-ac71-46f2-bf73-24fc3c008b6c"
#> [7] "cece4fc2-1fec-4bb5-a335-7252548e3f0b"

in context

dat %>% 
  select(title, key, doi)
#>                            title                                  key
#> 4            CAS Mammalogy (MAM) 6ce7290f-47f6-4046-8356-371f5b6749df
#> 5          CAS Ornithology (ORN) 4f29b6ab-20c0-4479-8795-4915bedcebd1
#> 6               CAS Botany (BOT) f934f8e2-32ca-46a7-b2f8-b032a4740454
#> 7          CAS Ichthyology (ICH) 5d6c10bd-ea31-4363-8b79-58c96d859f5b
#> 11          CAS Entomology (ENT) 14f3151a-e95d-493c-a40d-d9938ef62954
#> 13 CAS Invertebrate Zoology (IZ) 44bcde48-ac71-46f2-bf73-24fc3c008b6c
#> 14        CAS Herpetology (HERP) cece4fc2-1fec-4bb5-a335-7252548e3f0b
#>                    doi
#> 4  doi:10.15468/dhbozg
#> 5  doi:10.15468/ozz2u5
#> 6  doi:10.15468/7gudyo
#> 7  doi:10.15468/efh2ib
#> 11 doi:10.15468/3ibpmo
#> 13 doi:10.15468/tiac99
#> 14 doi:10.15468/bvoyqy

the CAS dataset identifiers are also included in this package, see ?gbif_datasets

iDigBio

There's no easy way to get iDigBio dataset identifers from their API, so we've included a dataset in the package with the identifiers for each dataset - some datasets have many identifiers.

idigbio_recordsets
#> $entomology
#> [1] "87c45c90-ba1d-409e-a9d7-9baf5a5cbb1c"
#> [2] "ded380b5-1ba2-4089-8e0c-0aa1b4140785"
#> 
#> $herpetology
#> [1] "51b958bb-9d5f-48d7-9a97-e372c0c747c3"
#> 
#> $ichthyology
#> [1] "beb74dc2-22ea-49e4-b1e3-bedb8e06e8f2"
#> 
#> $`invertebrate zoology & geology`
#> [1] "bd61c458-b865-4b05-9f1f-735c49066e55"
#> 
#> $ornithology
#> [1] "b8cbed64-5126-46bd-97aa-43627743aba7"
#> 
#> $mammalogy
#> [1] "14a8f79f-eab7-48da-ad50-bda142703820"
#> 
#> $botany
#> [1] "1ffce054-8e3e-4209-9ff4-c26fa6c24c2f"
#> [2] "8dc14464-57b3-423e-8cb0-950ab8f36b6f"
#> [3] "26f7cbde-fbcb-4500-80a9-a99daa0ead9d"

just botany

idigbio_recordsets$botany
#> [1] "1ffce054-8e3e-4209-9ff4-c26fa6c24c2f"
#> [2] "8dc14464-57b3-423e-8cb0-950ab8f36b6f"
#> [3] "26f7cbde-fbcb-4500-80a9-a99daa0ead9d"

ropenscilabs/spplit documentation built on Sept. 29, 2020, 3:05 a.m.