Problem pulling ranks below species from tropicos

[scelmendorf]

Hi,
I'm trying to pull info for a variety, that is in tropicos.

Here's an example:
Acroporium fuscoflavum var. baldwinii

If you follow the code below I think it illustrated the problem better than my verbal description could.

library (taxize)
thisWorksWell<-get_tpsid(sciname='Pinus contorta')
thisWorksWell
thisFailsEntirely<-get_tpsid(sciname='Acroporium fuscoflavum var. baldwinii')
thisFailsEntirely
thisAlmostWorks<-get_tpsid(sciname=gsub (' var.', '', 'Acroporium fuscoflavum var. baldwinii'))
thisAlmostWorks

why can't I get all of this?

change API key before runningexample

XMLq<-'http://services.tropicos.org/Name/Search?name=Acroporium+fuscoflavum+baldwinii&type=wildcard&apikey=MyAPIKeyThatImNotPostingOnGit&format=xml'
dataQ<-xmlParse(XMLq)
xmlData <- xmlToList(dataQ)
dataQ<-as.data.frame(t(data.frame(as.list(xmlData))))
dataQ$V1['Name.ScientificName']

[sckott]

Hi @scelmendorf - Thanks for the report. Tropicos has a few problems:

1. They don't allow a period in the query, even if it's URL encoded. The query fails on their server with a period. So i'm fixing that to replace periods with the url encoded equivalent. However, see 2 below
2. Tropicos doesn't like sub-specific rank names. That is, Acroporium fuscoflavum var. baldwinii' isn't found at all, but Acroporium fuscoflavum baldwinii' is found.

I am putting in some warnings to catch when users include periods and when var/subsp/etc. are included and updating documentation

[scelmendorf]

Thanks - that sounds great.
While you're at it wrt the warnings, I would look for
terminal:
sp.
sp

all forms of subspecies abbreviation
ssp.
subsp.
subspecies

all forms of variety
var.
varietas

and all forms of form
fo.
f.
forma

[sckott]

thanks for the additional things to look for, will do

[sckott]

@scelmendorf try again after reinstalling. let me know if it works as expected now