Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

query fails due to unmatched names #93

Open
snacktavish opened this issue Apr 23, 2024 · 2 comments
Open

query fails due to unmatched names #93

snacktavish opened this issue Apr 23, 2024 · 2 comments

Comments

@snacktavish
Copy link
Member

snacktavish commented Apr 23, 2024

> spp = c("Caprimulgus aegyptius","Vanellus tricolor","Recurvirostra americana","Centropus nigrorufus","Bombycilla cedrorum","Orthotomus cinereiceps","Ortygospiza atricollis", "Nasica longirostris","Terpsiphone viridis", "Myiothlypis signata","Atlapetes melanopsis","Idiopsar brachyurus","Rauenia bonariensis","Lessonia oreas","Tyrannus niveigularis"  ,"Rukia longirostra","Zosterops ponapensis","Ixobrychus involucris","Melanerpes pulcher","Picus viridanus","Cynanthus canivetii")
> bird_query = datelife::make_datelife_query(input = spp)
---> Phylo-processing 'input'.
* 'input' is not a phylogeny.
---> Making a DateLife query.
---> Runnning TNRS to match input names to reference taxonomy (OTT).
  |=====================================================================================================================================================================| 100%
Error in names(ott_ids) <- cleaned_names : 
  'names' attribute [21] must be the same length as the vector [20]
In addition: Warning message:
Cynanthus canivetii are not matched 
@snacktavish
Copy link
Member Author

I made a PR with a fix... but it's untested.

@LunaSare
Copy link
Member

Thanks! It does not break anything, but it leaves some NAs in the datelife_query, that look off. I need to:

  • make that remove nonmatches option accessible from earlier in the workflow
  • check why it is only dropping non matches on one vector

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants