| Type: | Package |
| Title: | R Client for the BIODATACR Biodiversity Data Platform of Costa Rica |
| Version: | 0.1.0 |
| Description: | Provides functions to query occurrence records, species information, and datasets from BIODATACR https://biodiversidad.go.cr, the national biodiversity information platform of Costa Rica managed by the Technical Office of CONAGEBIO, Costa Rica. Built on the Atlas of Living Australia (ALA) API infrastructure. |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| URL: | https://github.com/ManuelSpinola/rbiodatacr, https://manuelspinola.github.io/rbiodatacr/ |
| BugReports: | https://github.com/ManuelSpinola/rbiodatacr/issues |
| Suggests: | CoordinateCleaner, ggplot2, knitr, rmarkdown, sf, testthat (≥ 3.0.0) |
| Config/testthat/edition: | 3 |
| Imports: | cli, dplyr, httr, jsonlite, purrr |
| RoxygenNote: | 7.3.3 |
| VignetteBuilder: | knitr |
| Depends: | R (≥ 4.1.0) |
| LazyData: | true |
| Language: | en-US |
| NeedsCompilation: | no |
| Packaged: | 2026-04-28 01:22:28 UTC; manuel_nuevo |
| Author: | Manuel Spinola 
[aut, cre] |
| Maintainer: | Manuel Spinola <mspinola10@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2026-04-29 07:30:02 UTC |
Count occurrence records for a taxon
Description
Count occurrence records for a taxon
Usage
bdcr_count(taxon)
Arguments
taxon |
Character. Scientific name (e.g. '"Panthera onca"'). |
Value
Integer with the total number of available records.
Examples
## Not run:
bdcr_count("Panthera onca")
## End(Not run)
Count occurrence records for multiple taxa
Description
Count occurrence records for multiple taxa
Usage
bdcr_count_batch(taxa, wait = 1)
Arguments
taxa |
Character vector. Scientific names. |
wait |
Numeric. Seconds to pause between requests. Default 1. |
Value
A 'tibble' with columns 'taxon' and 'n_records'.
Examples
## Not run:
spp <- c("Tapirus bairdii", "Panthera onca")
bdcr_count_batch(spp)
## End(Not run)
Download occurrence records from BIODATACR
Description
Download occurrence records from BIODATACR
Usage
bdcr_occurrences(taxon, rows = 100, start = 0)
Arguments
taxon |
Character. Scientific name of the taxon. |
rows |
Integer. Maximum number of records to download. Default 100. |
start |
Integer. Starting record for pagination. Default 0. |
Value
A 'tibble' with columns: 'scientificName', 'vernacularName', 'decimalLatitude', 'decimalLongitude', 'year', 'month', 'basisOfRecord', 'dataResourceName', 'country', 'family', 'species', 'collector', 'license', 'geospatialKosher', 'taxonomicKosher'.
Examples
## Not run:
bdcr_occurrences("Panthera onca", rows = 50)
## End(Not run)
Download occurrence records for multiple taxa
Description
Download occurrence records for multiple taxa
Usage
bdcr_occurrences_batch(taxa, rows = 100, wait = 1)
Arguments
taxa |
Character vector. Scientific names. |
rows |
Integer. Records per taxon. Default 100. |
wait |
Numeric. Seconds to pause between requests. Default 1. |
Value
Named list of tibbles, one per taxon.
Examples
## Not run:
spp <- c("Tapirus bairdii", "Panthera onca")
bdcr_occurrences_batch(spp, rows = 50)
## End(Not run)
Quality check for occurrence records
Description
Adds a 'quality_flag' column to an occurrence tibble. Requires that 'geospatialKosher' and 'taxonomicKosher' are logical — a condition guaranteed by 'bdcr_occurrences()'.
Usage
bdcr_quality_check(df, min_year = 1950)
Arguments
df |
A 'tibble' of occurrence records (output of 'bdcr_occurrences()'). |
min_year |
Integer. Minimum acceptable year. Default 1950. |
Value
The same 'tibble' with an additional 'quality_flag' column. Possible values:
- '"ok"'
No issues detected.
- '"no_coords"'
Missing coordinates.
- '"geospatial_issue"'
'geospatialKosher == FALSE'.
- '"taxonomic_issue"'
'taxonomicKosher == FALSE'.
- '"old_record"'
Year before 'min_year'.
Examples
## Not run:
df <- bdcr_occurrences("Panthera onca", rows = 50)
bdcr_quality_check(df)
## End(Not run)
Search for taxonomic information of a species in BIODATACR
Description
Queries the BIE (Biodiversity Information Explorer) index of BIODATACR to retrieve taxonomic information for a species.
Usage
bdcr_species_search(name, rows = 10)
Arguments
name |
Character. Scientific name (may be a synonym or partial name). |
rows |
Integer. Maximum number of results. Default 10. |
Value
A 'tibble' with columns: 'name', 'guid', 'commonName', 'scientificName', 'rank', 'taxonomicStatus', 'nameComplete'.
Examples
## Not run:
bdcr_species_search("Panthera onca")
## End(Not run)
Costa Rica national boundary
Description
An 'sf' object with the national boundary of Costa Rica from GADM.
Usage
cr_outline
Format
An 'sf' object with 1 row and the following columns:
- GID_0
Country code (CRI)
- COUNTRY
Country name
- geometry
MULTIPOLYGON geometry