Skip to contents

Download and merge biodiversity data papers

Source: R/get_datapaper.R
get_datapaper.Rd

Downloads, reads, and merges published biodiversity data papers (see details for available options). The function allows downloading single or multiple datasets simultaneously, optionally filtering records by species name and saving the consolidated table to disk in different file formats.

Usage

get_datapaper(
  datapaper,
  species = NULL,
  save = FALSE,
  dir = NULL,
  file.format = "gz",
  overwrite = FALSE,
  verbose = TRUE
)

Arguments

datapaper

(character) vector with the names of the data papers to download. Valid options are: "atlantic", "brazil road-kill", "dryflor", "neotropical xenarthrans", and "neotroptree".

species

(character) optional species name or vector of species names to filter the dataset. Default is NULL (returns all species).

save

(logical) whether to save the merged output file to disk. If FALSE, files are downloaded to a temporary session directory. Default is FALSE.

dir

(character) directory path where the output file will be saved if save = TRUE. Default is NULL.

file.format

(character) file format to save the merged table. Valid options are "gz" (compressed CSV), "csv", or "rds". Default is "gz"

overwrite

(logical) whether to overwrite existing downloaded files in the destination directory. Default is FALSE

verbose

(logical) whether to display messages during function execution. Set to TRUE to enable display, or FALSE to run silently. Default is TRUE.

Value

A data.table containing the consolidated records from the selected data papers.

Details

Available datasets that can be requested in datapaper:

  • "atlantic": Atlantic data papers compilations.

  • "brazil road-kill": Brazil road-kill dataset.

  • "dryflor": Latin American and Caribbean Seasonally Dry Tropical Forests (DryFlor) dataset.

  • "neotropical xenarthrans": Neotropical Xenarthrans occurrence dataset.

  • "neotroptree": NeoTropTree tree species checklist database.

Note

When using any dataset retrieved by this function in publications or research reports, please cite the original authors. Use the function cite_datapaper() to obtain the complete bibliographic references.

Examples

 if (FALSE) { # \dontrun{
# Download Atlantic dataset
res <- get_datapaper(datapaper = "atlantic")

# Download multiple datasets and filter by a specific species
res_sp <- get_datapaper(
  datapaper = c("atlantic", "dryflor"),
  species = "Araucaria angustifolia")
} # }