Generate a species checklist from WCVP
Usage
wcvp_checklist(
taxon = NULL,
taxon_rank = c("species", "genus", "family", "order", "higher"),
area_codes = NULL,
synonyms = TRUE,
render_report = FALSE,
native = TRUE,
introduced = TRUE,
extinct = TRUE,
location_doubtful = TRUE,
hybrids = FALSE,
infraspecies = TRUE,
report_filename = NULL,
report_dir = NULL,
report_type = c("alphabetical", "taxonomic"),
wcvp_names = NULL,
wcvp_distributions = NULL
)Arguments
- taxon
Character. Taxon to be included. Defaults to NULL (no taxonomic filter; all taxa).
- 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 isNULL.- area_codes
Character. One or many WGSPRD level 3 region codes. Defaults to
NULL(global).- synonyms
Logical. Include synonyms in checklist (see Details)? Defaults to
TRUE.- render_report
Logical. Render the checklist as a markdown report? Defaults to
FALSE.- 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 toTRUE.- hybrids
Logical. Include hybrid species in checklist? Defaults to
FALSE.- infraspecies
Logical. Include hybrid species in checklist? Defaults to
TRUE.- report_filename
Character. Name for the HTML file. Defaults to taxon_area_type.html
- report_dir
Character. Directory for the HTML file to be saved in. Must be provided by user.
- report_type
Character; one of "alphabetical" (the default) or "taxonomic". Should the generated checklist be sorted alphabetically, or by taxonomic status?
- wcvp_names
A data frame of taxonomic names from WCVP version 7 or later. If
NULL(the default), names will be loaded fromrWCVPdata::wcvp_names.- wcvp_distributions
A data frame of distributions from WCVP version 7 or later. If
NULL(the default), distributions will be loaded fromrWCVPdata::wcvp_names.
Details
The synonyms argument can be used to limit names to those that are Accepted. If synonyms = TRUE then invalid, illegitimate and other non-accepted names are also included (i.e., the checklist is not limited to names for which taxon_status == "Synonym").
Two styles of checklist are supported in rWCVP - alphabetical and taxonomic.
In an alphabetical checklist, all names are arranged alphabetically with accepted names in bold, and synonyms are followed by their accepted name.
For a taxonomic checklist, names are grouped by their accepted names, and synonyms are listed beneath. Both types of checklist include author, publication and distribution information, though note that family headings are only supported in alphabetical checklists (due to the additional grouping requirement of the taxonomic format).
Examples
# These examples take >10 seconds to run and require 'rWCVPdata'
# \donttest{
if(requireNamespace("rWCVPdata")){
wcvp_checklist(taxon = "Myrtaceae", taxon_rank = "family", area = get_wgsrpd3_codes("Brazil"))
wcvp_checklist(taxon = "Ferns", taxon_rank = "higher", area = get_wgsrpd3_codes("New Zealand")) %>%
head()
}
#> ℹ Matches to input geography found at Country (Gallagher) and Region (Level 2)
#> ℹ Matches to input geography found at Country (Gallagher) and Region (Level 2)
#> higher order family plant_name_id ipni_id taxon_rank
#> 1 Ferns Polypodiales Aspleniaceae 3145698 146436-3 Subspecies
#> 2 Ferns Polypodiales Aspleniaceae 3145698 146436-3 Subspecies
#> 3 Ferns Polypodiales Aspleniaceae 3145698 146436-3 Subspecies
#> 4 Ferns Polypodiales Aspleniaceae 3145698 146436-3 Subspecies
#> 5 Ferns Polypodiales Aspleniaceae 3145698 146436-3 Subspecies
#> 6 Ferns Polypodiales Aspleniaceae 3197670 17572170-1 Subspecies
#> taxon_status genus_hybrid genus species_hybrid species
#> 1 Accepted <NA> Asplenium <NA> appendiculatum
#> 2 Accepted <NA> Asplenium <NA> appendiculatum
#> 3 Accepted <NA> Asplenium <NA> appendiculatum
#> 4 Accepted <NA> Asplenium <NA> appendiculatum
#> 5 Accepted <NA> Asplenium <NA> appendiculatum
#> 6 Accepted <NA> Asplenium <NA> appendiculatum
#> infraspecific_rank infraspecies parenthetical_author primary_author
#> 1 subsp. appendiculatum <NA> <NA>
#> 2 subsp. appendiculatum <NA> <NA>
#> 3 subsp. appendiculatum <NA> <NA>
#> 4 subsp. appendiculatum <NA> <NA>
#> 5 subsp. appendiculatum <NA> <NA>
#> 6 subsp. maritimum Brownsey Brownsey
#> publication_author place_of_publication volume_and_page first_published
#> 1 <NA> Unknown <NA> <NA>
#> 2 <NA> Unknown <NA> <NA>
#> 3 <NA> Unknown <NA> <NA>
#> 4 <NA> Unknown <NA> <NA>
#> 5 <NA> Unknown <NA> <NA>
#> 6 <NA> New Zealand J. Bot. 37: 369 (1999)
#> nomenclatural_remarks geographic_area
#> 1 <NA> SW. Victoria, Tasmania, New Zealand, Antipodean Is.
#> 2 <NA> SW. Victoria, Tasmania, New Zealand, Antipodean Is.
#> 3 <NA> SW. Victoria, Tasmania, New Zealand, Antipodean Is.
#> 4 <NA> SW. Victoria, Tasmania, New Zealand, Antipodean Is.
#> 5 <NA> SW. Victoria, Tasmania, New Zealand, Antipodean Is.
#> 6 <NA> New Zealand
#> lifeform_description climate_description
#> 1 <NA> <NA>
#> 2 <NA> <NA>
#> 3 <NA> <NA>
#> 4 <NA> <NA>
#> 5 <NA> <NA>
#> 6 perennial or epiphyte temperate
#> taxon_name taxon_authors
#> 1 Asplenium appendiculatum subsp. appendiculatum <NA>
#> 2 Asplenium appendiculatum subsp. appendiculatum <NA>
#> 3 Asplenium appendiculatum subsp. appendiculatum <NA>
#> 4 Asplenium appendiculatum subsp. appendiculatum <NA>
#> 5 Asplenium appendiculatum subsp. appendiculatum <NA>
#> 6 Asplenium appendiculatum subsp. maritimum (Brownsey) Brownsey
#> accepted_plant_name_id accepted_name
#> 1 3145698 Asplenium appendiculatum subsp. appendiculatum
#> 2 3145698 Asplenium appendiculatum subsp. appendiculatum
#> 3 3145698 Asplenium appendiculatum subsp. appendiculatum
#> 4 3145698 Asplenium appendiculatum subsp. appendiculatum
#> 5 3145698 Asplenium appendiculatum subsp. appendiculatum
#> 6 3197670 Asplenium appendiculatum subsp. maritimum
#> basionym_plant_name_id replaced_synonym_author homotypic_synonym
#> 1 NA <NA> NA
#> 2 NA <NA> NA
#> 3 NA <NA> NA
#> 4 NA <NA> NA
#> 5 NA <NA> NA
#> 6 3166250 <NA> NA
#> parent_plant_name_id powo_id hybrid_formula reviewed plant_locality_id
#> 1 3145697 146436-3 <NA> N 3507645
#> 2 3145697 146436-3 <NA> N 3507644
#> 3 3145697 146436-3 <NA> N 3507646
#> 4 3145697 146436-3 <NA> N 3507643
#> 5 3145697 146436-3 <NA> N 3507647
#> 6 3145697 17572170-1 <NA> N 4169299
#> continent_code_l1 continent region_code_l2 region area_code_l3
#> 1 5 AUSTRALASIA 50 Australia TAS
#> 2 5 AUSTRALASIA 50 Australia VIC
#> 3 5 AUSTRALASIA 51 New Zealand ATP
#> 4 5 AUSTRALASIA 51 New Zealand NZN
#> 5 5 AUSTRALASIA 51 New Zealand NZS
#> 6 5 AUSTRALASIA 51 New Zealand NZN
#> area introduced extinct location_doubtful occurrence_type
#> 1 Tasmania 0 0 0 native
#> 2 Victoria 0 0 0 native
#> 3 Antipodean Is. 0 0 0 native
#> 4 New Zealand North 0 0 0 native
#> 5 New Zealand South 0 0 0 native
#> 6 New Zealand North 0 0 0 native
#> in_geography endemic area_endemic
#> 1 FALSE FALSE FALSE
#> 2 FALSE FALSE FALSE
#> 3 TRUE FALSE FALSE
#> 4 TRUE FALSE FALSE
#> 5 TRUE FALSE FALSE
#> 6 TRUE FALSE TRUE
# }