Generate a summary table from the WCVP

Usage

wcvp_summary(
  taxon = NULL,
  taxon_rank = c("species", "genus", "family", "order", "higher"),
  area_codes = NULL,
  grouping_var = c("area_code_l3", "genus", "family", "order", "higher"),
  hybrids = FALSE,
  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 "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).
grouping_var: Character; one of "area_code_l3", "genus", "family","order" or "higher" specifying how the summary should be arranged. Defaults to area_code_l3.
hybrids: Logical. Include hybrid species in counts? Defaults to FALSE.
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

Data.frame with filtered data, or a gt table

Details

Valid values for rank 'higher' are 'Angiosperms', 'Gymnosperms', 'Ferns' and 'Lycophytes'. Note that grouping variable (if taxonomic) should be of a lower level than taxon and taxon_rank to produce a meaningful summary (i.e., it does not make sense to group a genus by genus, family or higher classification). Additionally, if the grouping variable is taxonomic then species occurrences are aggregated across the input area. This means that if a species is native to any of the input area (even if it is introduced or extinct in other parts) it is counted as 'Native'. Similarly, introduced occurrences take precedence over extinct occurrences. Note that in this type of summary table, 'Endemic' means endemic to the input area, not necessarily to a single WGSRPD Level 3 Area within the input area.

Examples

 # this example requires 'rWCVPdata'
if(requireNamespace("rWCVPdata")){
ferns <- wcvp_summary("Ferns", "higher", get_wgsrpd3_codes("New Zealand"), grouping_var = "family")
wcvp_summary_gt(ferns)
}
#> ℹ Matches to input geography found at Country (Gallagher) and Region (Level 2)
#> ℹ Aggregating occurrence types across input area ("New Zealand") - see `?wcvp_summary()` for details.


   Ferns of New Zealand 
    
Total number of species: 209
Number of regionally endemic species: 78
    
Family
      Native
      Endemic
      Introduced
      Extinct
      Total
    
Aspleniaceae
56
22
2

58
Cyatheaceae
11
8
1

12
Dennstaedtiaceae
12
2


12
Gleicheniaceae
9
1


9
Hymenophyllaceae
28
17


28
Lindsaeaceae
3
1


3
Marattiaceae
1



1
Marsileaceae
1



1
Ophioglossaceae
6
1


6
Osmundaceae
3
2
1

4
Polypodiaceae
35
16
8

43
Psilotaceae
6
1


6
Pteridaceae
18
6
1

19
Salviniaceae
1

1

2
Schizaeaceae
5
1


5

Family	Native	Endemic	Introduced	Total
Ferns of New Zealand
Total number of species: 209 Number of regionally endemic species: 78
Aspleniaceae	56	22	2	58
Cyatheaceae	11	8	1	12
Dennstaedtiaceae	12	2		12
Gleicheniaceae	9	1		9
Hymenophyllaceae	28	17		28
Lindsaeaceae	3	1		3
Marattiaceae	1			1
Marsileaceae	1			1
Ophioglossaceae	6	1		6
Osmundaceae	3	2	1	4
Polypodiaceae	35	16	8	43
Psilotaceae	6	1		6
Pteridaceae	18	6	1	19
Salviniaceae	1		1	2
Schizaeaceae	5	1		5