fwspp_review: Export species occurrence records in an 'fwspp' object to...

In adamdsmith/fwspp: Querying Biodiversity Databases on USFWS Properties

Export species occurrence records in an fwspp object to separate files for review

Description

Use this function to export species occurrence records into spreadsheets for review prior to parsing for inclusing into the FWSpecies database (https://sites.google.com/a/fws.gov/fwspecies/home-1)

Usage

fwspp_review(
  fwspp,
  out_dir = "./fwspp_review",
  overwrite = FALSE,
  verbose = TRUE
)

Arguments

fwspp	a fwspp object returned by fws_occ, **with taxonomy information added** (see Details). An output file will be created in out_dir for each property in fwspp.
out_dir	a non-empty character scalar of path to store an output file for each USFWS property in fwspp. The default is to use or create a fwspp_review directory in the current working directory.
overwrite	logical (default FALSE); overwrite existing files with the same name?
verbose	logical (default TRUE); provide detailed messaging during export process?

Details

This function **requires** that the fwspp object have taxonomy added (either via the taxonomy = TRUE argument during the call to fws_occ or subsequently via add_taxonomy). Reviewing records without additional taxonomic information (such as common name and general taxonomic groupings) is likely to be frustrating.

Value

NULL; Exports individual Excel file(s) to out_dir for the review of species occurrence observations

Regarding review of output spreadsheets

During review, users may modify the values for any observation from the taxon_code to evidence columns. Two columns in particular, however, will demand the most attention - accept_record and taxon_code.

Records without adequate documentation for inclusion in the FWSpecies database should have accept_record = No. Some observations may be set to accept_record = No by default because of ambiguous or misspelled scientific names.

Should a valid taxonomic match be found (e.g., by retrieving the appropriate taxon_code for the correct scientific name with fws_taxonomy), update the taxon_code in the spreadsheet and set accept_record = ModifiedTaxonCode. Setting accept_record = ModifiedTaxonCode means any taxonomic changes will be incorporated, and the record accepted, in the file subsequently created for submission to the FWSpecies database.

Changes to species taxonomy (taxon_code and sci_name) will be incorporated ONLY if taxon_code is corrected and accept_record = ModifiedTaxonCode.

Changes or additions to common names (com_name) will be accepted ONLY if accept_record = ModifiedTaxonCode, but taxon_code need not be changed for changes only to common name.

Changes to other columns (occurrence to evidence) will be incorporated as-is so long as accept_record = Yes or accept_record = ModifiedTaxonCode.

Records with accept_record = No are excluded.

Examples

## Not run: 
lowcountry <- find_fws(c("romain", "santee", "ace basin", "waccamaw"))
lc <- fws_occ(fws = lowcountry)
fwspp_review(lc)

## End(Not run)

adamdsmith/fwspp documentation built on May 14, 2024, 10:28 a.m.