wcvp_occ_mat {rWCVP} | R Documentation |
Generate occurrence matrix for taxa and areas
Description
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 |
area_codes |
Character. One or many WGSPRD level 3 region codes. Defaults to |
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 |
wcvp_distributions |
A data frame of distributions from WCVP version 7 or later.
If |
Details
See here for an example of how this output can be formatted for publication.
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.
Examples
# this example requires 'rWCVPdata'
if(requireNamespace("rWCVPdata")){
wcvp_occ_mat(
taxon = "Poa", taxon_rank = "genus",
area = c("TAS", "VIC", "NSW"), introduced = FALSE
)
}