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gbresolve function from the geiger package

2 messages · Nomi Hadar

Nomi Hadar
# 
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
2 days later
Nomi Hadar
# 
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>: