Last chance! 50% off unlimited learning
Sale ends in
Return the leaf taxa for a taxonomy()
or taxmap()
object. Leaf taxa are taxa
with no subtaxa.
obj$leaves(subset = NULL, recursive = TRUE, simplify = FALSE, value = "taxon_indexes") leaves(obj, subset = NULL, recursive = TRUE, simplify = FALSE, value = "taxon_indexes")
The taxonomy()
or taxmap()
object containing taxon
information to be queried.
Taxon IDs, TRUE/FALSE vector, or taxon indexes to find leaves for.
Default: All taxa in obj
will be used. Any variable name that appears in
all_names()
can be used as if it was a vector on its own.
(logical
or numeric
) If FALSE
, only return the
leaves if they occur one rank below the target taxa. If TRUE
, return all of the
leaves for each taxon. Positive numbers indicate the number of
recursions (i.e. number of ranks below the target taxon to return). 1
is
equivalent to FALSE
. Negative numbers are equivalent to TRUE
.
(logical
) If TRUE
, then combine all the results into a
single vector of unique values.
What data to return. This is usually the name of column in a
table in obj$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.
character
Other taxonomy indexing functions:
branches()
,
internodes()
,
roots()
,
stems()
,
subtaxa()
,
supertaxa()
# NOT RUN {
# Return indexes of leaf taxa
leaves(ex_taxmap)
# Return indexes for a subset of taxa
leaves(ex_taxmap, subset = 2:17)
leaves(ex_taxmap, subset = taxon_names == "Plantae")
# Return something besides taxon indexes
leaves(ex_taxmap, value = "taxon_names")
leaves(ex_taxmap, subset = taxon_ranks == "genus", value = "taxon_names")
# Return a vector of all unique values
leaves(ex_taxmap, value = "taxon_names", simplify = TRUE)
# Only return leaves for their direct supertaxa
leaves(ex_taxmap, value = "taxon_names", recursive = FALSE)
# }
Run the code above in your browser using DataLab