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

Description Usage Arguments Details Value Regarding review of output spreadsheets Examples

View source: R/fwspp_review.R

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

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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 nps_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

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## 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 April 3, 2018, 12:02 p.m.