In implementing this fix, a temporary aligned_name field is created that captures the string for the taxon name and this is formatted into the complete aligned_name element in a second line of code, removing duplicate code.
taxonomic references (taxonomic_ref) was not being explicitly assigned in many matches, depending upon an additional step of sourcing this information from the resources. Since the matches are explicitly made on names from specific resources, these are now always assigned when a match is made.
Genus-level alignments for hybrid, spp aff, "/" and "--" taxa were not being turned off for APNI taxa
The current version has been tested for a list of 225 taxon names that includes at least 2 name strings that are picked up by each of the 50 possible matches.
matches now pick up all variants previously listed in issues as failing (see issue https://github.com/traitecoevo/APCalign/issues/5, issue https://github.com/traitecoevo/APCalign/issues/44, issue https://github.com/traitecoevo/APCalign/issues/97)
previously a few genus-level matches were matching to
cleanedNameinstead ofcanonicalName, resulting in matches to synonymous terms (issue https://github.com/traitecoevo/APCalign/issues/113)as described in issue https://github.com/traitecoevo/APCalign/issues/114, In commit https://github.com/traitecoevo/APCalign/commit/8aabbc865da6efc86f9db67394b40f0fb72c32e5 there was an error introduced to all matches where an ifelse() statement was included to created the aligned_name. This has now been fixed.
In implementing this fix, a temporary
aligned_namefield is created that captures the string for the taxon name and this is formatted into the completealigned_nameelement in a second line of code, removing duplicate code.taxonomic references (
taxonomic_ref) was not being explicitly assigned in many matches, depending upon an additional step of sourcing this information from the resources. Since the matches are explicitly made on names from specific resources, these are now always assigned when a match is made.Genus-level alignments for hybrid, spp aff, "/" and "--" taxa were not being turned off for APNI taxa
The current version has been tested for a list of 225 taxon names that includes at least 2 name strings that are picked up by each of the 50 possible matches.