rbiodatacr

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).

Installation

remotes::install_github("ManuelSpinola/rbiodatacr")

Main functions

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

Basic usage

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)

Complete workflow

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)

About BIODATACR

BIODATACR is built on the infrastructure of the Atlas of Living Australia (ALA).

License

Logo

Tapir silhouette by Gabriela Palomo-Munoz via PhyloPic, licensed under CC BY 3.0.