reflora_indets

Documentation for reflora_indets() from the refloraR package.

refloraR::reflora_indets()

Description {

Retrieves occurrence records for indeterminate specimens (e.g., identified

only to family or genus level) from the

\href

{ https://ipt.jbrj.gov.br/reflora/ }

{ REFLORA Virtual Herbarium }

hosted by the \href

{ https://www.gov.br/jbrj/pt-br }

{ Rio de Janeiro Botanical Garden } .

The function automatically downloads and parses Darwin Core Archive (DwC-A)

files, applies optional filters by taxon, herbarium, state, and year, and

exports the results if desired.

}

Details {

This function supports downloading and processing Darwin Core Archive (DwC-A)

files directly from the REFLORA repository. It allows for flexible filtering

by taxon, herbarium, locality (Brazilian states), and collection year(s). The

level parameter enables filtering for indeterminate records such as those

identified only to FAMILY or GENUS rank. The function uses helper functions

like .arg_check_herbarium() and .filter_occur_df() to validate inputs and

refine the occurrence records. If path is not provided, the function will

automatically manage downloading and storing fresh DwC-A archives.

}

Arguments

Argument	Description

"FAMILY", "GENUS", or both. Defaults to NULL to include all indeterminate ranks. } | { level } { Character vector. Filter by taxonomic level. Accepted values: "FAMILY", "GENUS", or both. Defaults to NULL to include all indeterminate ranks. } | | { herbarium } { Character vector. Herbarium codes (e.g., "RB", "SP") in uppercase. Use NULL to include all herbaria. } | { herbarium } { Character vector. Herbarium codes (e.g., "RB", "SP") in uppercase. Use NULL to include all herbaria. } | | { repatriated } { Logical. If | { repatriated } { Logical. If | | { taxon } { Character vector. Specific taxon names to filter by (e.g., "Fabaceae"). } | { taxon } { Character vector. Specific taxon names to filter by (e.g., "Fabaceae"). } | | { state } { Character vector. Brazilian state full name or abbreviations (e.g., "BA", "SP") to filter by locality. } | { state } { Character vector. Brazilian state full name or abbreviations (e.g., "BA", "SP") to filter by locality. } | | { recordYear } { Character or numeric vector. A single year (e.g., "2001") or a range (e.g., c("2000", "2022")). } | { recordYear } { Character or numeric vector. A single year (e.g., "2001") or a range (e.g., c("2000", "2022")). } | | { reorder } { Character vector. Reorder output by columns. Defaults to: c("herbarium", "taxa", "collector", "area", "year"). } | { reorder } { Character vector. Reorder output by columns. Defaults to: c("herbarium", "taxa", "collector", "area", "year"). } | | { path } { Character. Path to existing REFLORA dwca files. If NULL, downloads fresh data. } | { path } { Character. Path to existing REFLORA dwca files. If NULL, downloads fresh data. } | | { updates } { Logical. If TRUE (default), checks for updated DwC-A files from REFLORA. } | { updates } { Logical. If TRUE (default), checks for updated DwC-A files from REFLORA. } | | { verbose } { Logical. If TRUE (default), prints progress messages to the console. } | { verbose } { Logical. If TRUE (default), prints progress messages to the console. } | | { save } { Logical. If TRUE (default), saves the results to a CSV file. } | { save } { Logical. If TRUE (default), saves the results to a CSV file. } | | { dir } { Character. Directory path to save output files. Default: "reflora_indets". } | { dir } { Character. Directory path to save output files. Default: "reflora_indets". } | | { filename } { Character. Name of the output file (without extension). Default: "reflora_indets_search". } |

{ filename } { Character. Name of the output file (without extension). Default: "reflora_indets_search". } |

Value {

A data.frame containing filtered specimen records for the selected

indeterminate specimens and criteria. If save = TRUE, a CSV file with the

results will be written to the specified dir, and a log.txt file will be

created or appended in the same directory summarizing the download session and

key statistics (total records, breakdowns by herbarium, family, genus, country,

and state).

}

Examples

 \examples
{


\dontrun
{


# Retrieve indeterminate records for Fabaceae and Ochnaceae from all herbaria

reflora_indets(taxon = c("Fabaceae", "Ochnaceae"),

               level = "FAMILY",

               save = TRUE,

               dir = "reflora_indets",

               filename = "fabaceae_ochnaceae_records")



# Filter by specific herbarium and state

reflora_indets(taxon = "Fabaceae",

               herbarium = "RB",

               state = c("BA", "MG"),

               recordYear = c("1990", "2022"))

}




}