o.k I found that I have to update my local copy of ncbi, but when I do: *ncbit(update=TRUE)*
I get: *"NCBI GenBank taxonomy assembled 2013-03-29"* Why it was not updated? Thanks Nomi 2016-06-20 14:11 GMT+03:00 Nomi Hadar <hadar.n...@gmail.com>: > Hello, > > I have troubles with the gbresolve function from the *geiger *package, > which works with the NCBI taxonomy. > When I use it, there are genera that are not found although they *do > appear *in the NCBI taxonomy browser. > <http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/> > > for example, when I run: > > library("ape") > library("geiger") > > genus = "Christia" > gbresolve(genus, rank= "genus", within = "Fabaceae") > > ("Christia" is a genus within a plants group called Fabaceae) > > I get: > > Error in tmp[[idx]] : subscript out of bounds > In addition: Warning messages: > 1: In FUN(X[[i]], ...) : Attempt one of the following: > Bacterium purifaciens Christiansen 1917 > ... > ... > 2: In gbresolve.default(genus, rank = "genus", within = "Fabaceae") : > The following taxa were not encountered in the NCBI taxonomy: > Christia > > > And so for other genera such as "Pycnospora" / "Solori" / > "Thailentadopsis" and more. > You can see that "Christia" appears in browser > <http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi>, and so I > expect to get "Christia vespertilionis" as result. > > Why is that? > > Thank you very much! > Nomi > > > -- > *Nomi Hadar* > > -- *Nomi Hadar* [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
