Closed mjwestgate closed 3 years ago
This has been addressed with the following steps:
level_down()
to skip past ranks labelled informal
or unranked
level_down
from using data.frame
to list
, enabling data on intermediate nodes to be storedlist
to tree using data.tree
to allow extraction of richer node-level datasearch_taxonomy
to ala_taxonomy
for consistency with galah
naming conventions for data-returning functionsala_taxonomy
to require object of class ala_id
(via select_taxa()
) for consistency with with other ala_
functions
In version 1.3.0, the following code fails to detect a lot of taxa, apparently because it stops searching at nodes labeled
informal
orunranked
. This leads to some very visible problems, e.g.....fails to return any of the vertebrate classes, because they are all listed under the informal rank
Gnathostomata
. This appears to occur because the recursive function insidesearch_taxonomy
(level_down()
) checks againstfind_ranks()
before proceeding, andinformal
is not listed infind_ranks
. Suggest allowinglevel_down
to recognise informal nodes.