Get the ids of all ancestors of some taxa

Get the ids of all ancestors of some taxa

ancestors(taxon_ids, taxo, n = Inf)

Arguments

taxon_ids

internal, numeric ids of the taxa.
taxo

a taxonomy data.frame, typically from extract_taxo().
n

maximum number of levels to look up; n=1 gives the parents, n=2 gives the parents and the grand-parents, etc.

Value

A vector of taxonomic ids containing the input taxon_ids and all their ancestors. With a single taxon in taxon_ids, the ancestors are in ordered from the taxon to the root of the tree: they define the lineage. When taxon_ids contains multiple taxa, the order is non-trivial.

Details

Even with n=1, the function is different from parent() because it returns all unique parents for all elements of taxon_ids, not one parent per element.

See also

Other taxonomy-related functions: as.taxo(), children(), descendants(), extract_taxo(), is_leaf(), lineage(), parent(), taxo_id(), taxo_name()

Examples

print(as.Node(taxo), "id")

#>             levelName id
#> 1 #                   NA
#> 2  °--living           1
#> 3      ¦--fish         2
#> 4      ¦   °--egg      4
#> 5      °--mollusc      3
#> 6          ¦--snail    5
#> 7          ¦   °--egg  7
#> 8          °--squid    6
ancestors(5, taxo)

#> [1] 1 3 5
ancestors(1, taxo)

#> [1] 1
ancestors(NA, taxo)

#> [1] NA
ancestors(1:7, taxo)

#> [1] 1 3 2 5 4 6 7
ancestors(6, taxo, n=1)

#> [1] 3 6
ancestors(6, taxo, n=2)

#> [1] 1 3 6
ancestors(6, taxo, n=3)

#> [1] 1 3 6
ancestors(6, taxo, n=10)

#> [1] 1 3 6
# NB:
ancestors(5:6, taxo, n=1)

#> [1] 3 5 6
parent(5:6, taxo)

#> [1] 3 3