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Standardize species names to AFS codes

Source: R/standardize-species.R
standardize_species.Rd

Maps free-text species names in a data frame to canonical American Fisheries Society (AFS) species codes, appending a species_code column. Matching is case-insensitive and checks both exact common names and comma-separated aliases bundled with the package. Values that already look like a known AFS code (all-uppercase, 3 characters) are passed through directly. Unmatched values are left as NA with a cli warning listing the unrecognised inputs.

Usage

standardize_species(
  data,
  species_col = "species",
  lookup = "AFS",
  fuzzy = TRUE,
  keep_original = TRUE
)

Arguments

data

A data frame containing a species name column.

species_col

Character scalar naming the column that holds species names. Default "species".

lookup

Character scalar identifying the code system to use. Currently only "AFS" (default) is supported; passing any other value raises an error.

fuzzy

Logical. If TRUE (default), aliases (common abbreviations and alternate names) are also searched. Set FALSE for strict common-name matching only.

keep_original

Logical. If TRUE (default), the original species_col column is preserved unchanged. Set FALSE to drop it.

Value

data with an additional species_code character column appended. Unmatched rows receive NA_character_.

See also

Other "Reporting & Diagnostics": adjust_nonresponse(), check_completeness(), compare_variance(), flag_outliers(), season_summary(), summarize_by_angler_type(), summarize_by_day_type(), summarize_by_method(), summarize_by_species_sought(), summarize_by_trip_length(), summarize_cws_rates(), summarize_hws_rates(), summarize_length_freq(), summarize_refusals(), summarize_successful_parties(), summarize_trips(), summary.creel_estimates(), validate_creel_data(), validate_design(), validate_incomplete_trips(), validation_report(), write_estimates()

Examples

interviews <- data.frame(
  date    = as.Date(c("2024-06-01", "2024-06-02", "2024-06-03")),
  species = c("walleye", "Largemouth Bass", "UNKNOWN"),
  kept    = c(2L, 1L, 0L)
)
standardize_species(interviews)
#> Warning: 1 species value(s) could not be matched to an
#> AFS code and will be "NA":
#> • "UNKNOWN"
#>         date         species kept species_code
#> 1 2024-06-01         walleye    2          WAE
#> 2 2024-06-02 Largemouth Bass    1          LMB
#> 3 2024-06-03         UNKNOWN    0         <NA>