Test if taxa are stems in a taxonomy() or taxmap() object. Stems are taxa from the roots() taxa to the first taxon with more than one subtaxon. These can usually be filtered out of the taxonomy without removing any information on how the remaining taxa are related.

obj$is_stem()
is_stem(obj)

Arguments

obj

The taxonomy() or taxmap() object.

Value

A logical of length equal to the number of taxa.

See also

Examples

# Test which taxon IDs correspond to stems is_stem(ex_taxmap)
#> b c d e f g h i j k l m n #> FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE #> o p q r #> FALSE FALSE FALSE FALSE
# Filter out stems filter_taxa(ex_taxmap, ! is_stem)
#> <Taxmap> #> 15 taxa: b. Mammalia, d. Felidae ... q. lycopersicum, r. tuberosum #> 15 edges: NA->b, b->d, b->e, b->f ... j->o, k->p, l->q, l->r #> 4 data sets: #> info: #> # A tibble: 6 x 4 #> taxon_id name n_legs dangerous #> <chr> <chr> <dbl> <lgl> #> 1 m tiger 4 TRUE #> 2 n cat 4 FALSE #> 3 o mole 4 FALSE #> # … with 3 more rows #> phylopic_ids: a named vector of 'character' with 6 items #> m. e148eabb-f138-43[truncated] ... r. 63604565-0406-46[truncated] #> foods: a list of 6 items named by taxa: #> m, n, o, p, q, r #> abund: #> # A tibble: 8 x 5 #> taxon_id code sample_id count taxon_index #> <chr> <fct> <fct> <dbl> <int> #> 1 m T A 1 1 #> 2 n C A 2 2 #> 3 o M B 5 3 #> # … with 5 more rows #> 1 functions: #> reaction