[R-sig-eco] Package bio.infer: get.taxonomic() hangs R after editing taxa list

[Eduard Szöcs]

Hai Rich,

Have a look at our recently released taxize-package.
However we some some problems with the ITIS-API, too. (Maybe some server 
issues?)
See https://github.com/ropensci/taxize_/issues/72

However with taxize you can also query the NCBI taxonomy browser as 
alternative:

df <- read.table(header = TRUE, as.is = TRUE, text = 'SVN              
Taxon CountValue
1 WP220110711  Zaitzevia.parvula        484
2 WP220110711           Tvetenia        109
3 WP220110711        Tubificidae       1054
4 WP220110711            Sweltsa         11
5 WP220110711 Suwallia.pallidula         32
6 WP220110711     Stempellinella         11 ')
df$Taxon <- gsub("\\.", " ", df$Taxon)

require(taxize)

#query itis
classification(get_tsn(df$Taxon))
### This may fail sometimes. 'Connection reset by peer'
### we are working at it:
### see https://github.com/ropensci/taxize_/issues/72

# query ncbi taxonomy-browser instead
classification(get_uid(df$Taxon))


Hope this helps,

Eduard



On 12/11/2012 11:08 PM, Rich Shepard wrote:
> On Mon, 10 Dec 2012, Sarah Goslee wrote:
>
>> ... get.taxonomic() no longer has an outputFile argument.
>
>   I've read the get.taxonomic() description in bio.infer.pdf and it works
> ... to a point. There are 3 taxa currently not in the ITIS database (a
> freshwater worm, a midge, and one chironomid for which I can't track down
> the genus). The first two are going through the validation process and 
> will
> be added to ITIS Real Soon Now. In the meantime, I don't know how to
> proceed. So I've copied Lester Yuan on this message.
>
>   I tell get.taxonomic() that I'm finished editing and it flashes a 
> Tcl/Tk
> window then ists the taxa not in the data base, but does not return the R
> prompt:
>
>> jerall <- get.taxonomic(bioinfer)
> The following taxa are not in ITIS:
> EISENIELLA
> RADOTANYPUS
> ZIATZEVIA
>
>   I've not found a key combination that lets me gracefully exit R (or 
> emacs
> for that matter); I can only kill the process. Nothing I've seen in 
> the help
> files appears relevant.
>
>   Any suggestions?
>
> Rich
>
> _______________________________________________
> R-sig-ecology mailing list
> R-sig-ecology at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>