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rbiodatacr is an R client for querying BIODATACR, the national
biodiversity information platform of Costa Rica managed by the Technical
Office of CONAGEBIO (Comision Nacional para la Gestion de la
Biodiversidad, Costa Rica).
remotes::install_github("ManuelSpinola/rbiodatacr")| Function | Description |
|---|---|
bdcr_count() |
Count available records for a taxon |
bdcr_count_batch() |
Count records for multiple taxa |
bdcr_occurrences() |
Download occurrence records for a taxon |
bdcr_occurrences_batch() |
Download occurrence records for multiple taxa |
bdcr_species_search() |
Search taxonomic information in the BIE index |
bdcr_quality_check() |
Evaluate record quality and assign flags |
library(rbiodatacr)
# Check data availability
bdcr_count("Panthera onca")# Download occurrence records
df <- bdcr_occurrences("Panthera onca", rows = 50)
dplyr::glimpse(df)# Query for multiple species
species <- c("Tapirus bairdii", "Panthera onca", "Ara ambiguus")
counts <- bdcr_count_batch(species)
counts# Quality control
df_qc <- bdcr_quality_check(df)
dplyr::count(df_qc, quality_flag, sort = TRUE)library(rbiodatacr)
library(dplyr)
# 1. Explore data availability
species <- c("Tapirus bairdii", "Panthera onca",
"Ara ambiguus", "Bradypus variegatus")
counts <- bdcr_count_batch(species)
# 2. Download species with sufficient data
with_data <- filter(counts, n_records >= 10)
occ_list <- bdcr_occurrences_batch(
taxa = with_data$taxon,
rows = 200
)
# 3. Quality control and consolidate
df_final <- purrr::map(occ_list, bdcr_quality_check) |>
bind_rows(.id = "taxon") |>
filter(quality_flag == "ok",
!is.na(decimalLatitude),
!is.na(decimalLongitude))
# 4. Summary
df_final |>
count(taxon, sort = TRUE) |>
rename(clean_records = n)BIODATACR is built on the infrastructure of the Atlas of Living Australia (ALA).
MIT © Manuel Spinola
Tapir silhouette by Gabriela Palomo-Munoz via PhyloPic, licensed under CC BY 3.0.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.