R help - Jun 2016 - gbresolve function from the geiger package

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*

	[[alternative HTML version deleted]]

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.nomi at 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]]