Generate occurrence matrix for taxa and areas

Usage

wcvp_occ_mat(
  taxon = NULL,
  taxon_rank = c("species", "genus", "family", "order", "higher"),
  area_codes = NULL,
  native = TRUE,
  introduced = TRUE,
  extinct = TRUE,
  location_doubtful = TRUE,
  wcvp_names = NULL,
  wcvp_distributions = NULL
)

Arguments

taxon: Character. One or many taxa to be included. Defaults to NULL (all species)
taxon_rank: Character. One of "species", "genus", "family", "order" or "higher", giving the rank of the value/s in taxon. Must be specified unless taxon is NULL.
area_codes: Character. One or many WGSPRD level 3 region codes. Defaults to NULL (global).
native: Logical. Include species occurrences not flagged as introduced, extinct or doubtful? Defaults to TRUE.
introduced: Logical. Include species occurrences flagged as introduced? Defaults to TRUE.
extinct: Logical. Include species occurrences flagged as extinct? Defaults to TRUE.
location_doubtful: Logical. Include species occurrences flagged as location doubtful? Defaults to TRUE.
wcvp_names: A data frame of taxonomic names from WCVP version 7 or later. If NULL, names will be loaded from rWCVPdata::wcvp_names.
wcvp_distributions: A data frame of distributions from WCVP version 7 or later. If NULL, distributions will be loaded from rWCVPdata::wcvp_names.

Value

A data.frame containing the taxon_name and plant_name_id

of all species that are present in the area, plus one variable for each WGSPRD level 3 region in area, with species presences marked as 1 and absences marked as 0.

Details

See here for an example of how this output can be formatted for publication.

Examples

 # this example requires 'rWCVPdata'
if(requireNamespace("rWCVPdata")){
wcvp_occ_mat(
  taxon = "Poa", taxon_rank = "genus",
  area = c("TAS", "VIC", "NSW"), introduced = FALSE
)
}
#> # A tibble: 37 × 5
#>    plant_name_id taxon_name          NSW   TAS   VIC
#>            <dbl> <chr>             <dbl> <dbl> <dbl>
#>  1        435044 Poa affinis           1     0     1
#>  2        469193 Poa amplexicaulis     0     0     1
#>  3        435565 Poa cheelii           1     0     0
#>  4        435598 Poa clelandii         0     1     1
#>  5        435599 Poa clivicola         1     1     1
#>  6        435658 Poa costiniana        1     1     1
#>  7        435661 Poa crassicaudex      0     0     1
#>  8        435797 Poa drummondiana      0     0     1
#>  9        435841 Poa ensiformis        1     0     1
#> 10        435878 Poa fawcettiae        1     1     1
#> # ℹ 27 more rows