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.