Convert forest plot census data into a herbarium spreadsheet format

Here we present a complete guide to the fp_herb_converter() function of the forplotR package. This function allows users to convert plot census specimen records to a herbarium spreadsheet Format from the Rio de Janeiro Botanical Garden’s JABOT herbarium collection spreadsheet It also supports for BRAHMS or other customized herbarium spreadsheet format (user-specified column mapping).

Function Overview

The fp_herb_converter() function convert forest plot census data into a herbarium spreadsheet format by reading a ForestPlots-format field dataset and an herbarium template, and outputs a filled herbarium data frame.

Arguments

Argument Description
forestplots_file_path File path to the forestplots dataset.
herb_file_path File path of the herbarium empty template dataset.
language Language for output metadata. Default is "en", options are "en", "pt" and "es".
herbarium_format Format of the herbarium dataset. Default is "jabot", additional options is “brahms”, “custom” herbarium format, where column names must be specified by the user.
country Country where the data was collected. Default is "Brazil".
majorarea State where the data was collected
minorarea Municipality where the data was collected.
protectedarea Name of the protected area (if applicable).
locnotes A character vector of herbarium acronyms (e.g., "RB", "K"). Use NULL to download all collections.
project Logical. If FALSE, repatriated herbaria will be skipped. Use jabot_summary() to identify them.
collector Logical. If TRUE, messages describing download progress will be shown.
addcoll Directory path to save the files. Default is "jabot_download".
lat A character vector of herbarium acronyms (e.g., "RB", "K"). Use NULL to download all collections.
lon Logical. If FALSE, repatriated herbaria will be skipped. Use jabot_summary() to identify them.
alt Logical. If download progress will be shown.
dir Directory path to save the files. Default is "Results_rainfor_herb".
filename Directory path to save the files. Default is "rainfor_to_herb".

Convert forestplot dataset into JABOT spreadsheet format

Use the function with default settings to convert the fieldsheet into JABOT spreadsheet herbarium format

fp_herb_converter(
                       forestplots_file_path = NULL,
                       herb_file_path = NULL,
                       language = "en",
                       herbarium_format = "jabot",
                       country = "Brazil",
                       majorarea = NULL,
                       minorarea = NULL,
                       protectedarea = NULL,
                       locnotes = NULL,
                       project = NULL,
                       collector = NULL,
                       addcoll = NULL,
                       lat = NULL,
                       long = NULL,
                       alt = NULL,
                       dir = "Results_rainfor_herb",
                       filename = "rainfor_to_herb"
)

Download Specimens from Selected Collections

Specify collection codes with the herbarium argument:

jabot_download(
  herbarium = c("AFR", "R", "RB"),
  verbose = TRUE,
  dir = "jabot_download"
)

Skipping Repatriated Collections

To exclude collections marked as repatriated:

jabot_download(
  repatriated = FALSE,
  verbose = TRUE,
  dir = "jabot_download"
)

Example: Custom Directory Without Verbose Messages

jabot_download(
  herbarium = "RB",
  dir = "custom_directory"
)

Additional Tips

  • Use fp_herb_converter to inspect which collections are available and whether they are repatriated.
  • Ensure internet access is available when running jabot_download().
  • Review the contents of the downloaded folder to verify occurrence.txt and metadata presence.

See Also