Get stem taxa

Return the stem taxa for a taxonomy() or a taxmap() object. Stem taxa are all those from the roots to the first taxon with more than one subtaxon.

obj$stems(subset = NULL, simplify = FALSE,
  value = "taxon_indexes", exclude_leaves = FALSE)
stems(obj, subset = NULL, simplify = FALSE,
  value = "taxon_indexes", exclude_leaves = FALSE)

Arguments

obj	The taxonomy() or taxmap() object containing taxon information to be queried.
subset	Taxon IDs, TRUE/FALSE vector, or taxon indexes to find stems for. Default: All taxa in obj will be used. Any variable name that appears in all_names() can be used as if it was a vector on its own.
value	What data to return. This is usually the name of column in a table in obj$data. Any result of all_names(obj) can be used, but it usually only makes sense to data that corresponds to taxa 1:1, such as taxon_ranks(). By default, taxon indexes are returned.
simplify	(logical) If TRUE, then combine all the results into a single vector of unique values.
exclude_leaves	(logical) If TRUE, the do not include taxa with no subtaxa.

Value

character

See also

Other taxonomy indexing functions: branches(), internodes(), leaves(), roots(), subtaxa(), supertaxa()

Examples

# Return indexes of stem taxa
stems(ex_taxmap)
#> $b
#> named integer(0)
#> 
#> $c
#> c g 
#> 2 6 
#> 

# Return indexes for a subset of taxa
stems(ex_taxmap, subset = 2:17)
#> $c
#> c g 
#> 2 6 
#> 
#> $d
#> named integer(0)
#> 
#> $e
#>  e  j  o 
#>  4  9 14 
#> 
#> $f
#>  f  k  p 
#>  5 10 15 
#> 

# Return something besides taxon indexes
stems(ex_taxmap, value = "taxon_names")
#> $b
#> named character(0)
#> 
#> $c
#>            c            g 
#>    "Plantae" "Solanaceae" 
#> 

# Return a vector instead of a list
stems(ex_taxmap, value = "taxon_names", simplify = TRUE)
#>            c            g 
#>    "Plantae" "Solanaceae"