Count the number of taxa per rank in a taxonomy_graph and return
the result as a tibble.
Details
If by_rank is not used, the number of taxa is counted in the complete
graph or in the subgraph specified by subgraph.
by_rank can be used to count ranks grouped by the taxa of a given rank.
In this case, each row will correspond to a taxon of the requested rank
and each column will correspond to a rank.
Examples
file <- get_example_taxonomy_file()
taxonomy <- read_taxonomy(file)
# count the complete graph
count_ranks(taxonomy)
#> # A tibble: 10 × 2
#> rank n
#> <ord> <int>
#> 1 Ordnung 1
#> 2 Unterordnung 2
#> 3 Überfamilie 1
#> 4 Familie 14
#> 5 Unterfamilie 2
#> 6 Tribus 2
#> 7 Gattung 13
#> 8 Art 57
#> 9 Unterart 3
#> 10 ohne Rang 1
# count only the cats
count_ranks(taxonomy, subgraph = "Katzen")
#> # A tibble: 4 × 2
#> rank n
#> <ord> <int>
#> 1 Familie 1
#> 2 Unterfamilie 2
#> 3 Gattung 3
#> 4 Art 12
# count caniformia by family
count_ranks(taxonomy, "Hundeartige", by_rank = "Familie")
#> # A tibble: 9 × 5
#> Familie Tribus Gattung Art Unterart
#> <chr> <int> <int> <int> <int>
#> 1 Hunde 2 2 8 0
#> 2 Bären 0 1 8 3
#> 3 Walrosse 0 0 1 0
#> 4 Hundsrobben 0 0 4 0
#> 5 Ohrenrobben 0 1 3 0
#> 6 Marder 0 3 10 0
#> 7 Skunks 0 0 1 0
#> 8 Ailuridae 0 1 0 0
#> 9 Kleinbären 0 1 1 0