[R-sig-eco] error message in package "FD", function dbFD ()

[Novack-Gottshall, Philip M.]

Laura,

Does one of your species names have a blank space at the end of it
(that's invisible to your eye, but seen by R)?

Without your actual data files, I can't diagnose the exact details. But
if you "reveal" the dbFD() code [command line: > dbFD] and search for
your error message, you'll find that somehow the row names for your
transposed "a" file are not identical to the row names for your "x" file.

Try the following to confirm:
identical(row.names(x), row.names(t(a)))

I'm guess this will yield "FALSE" (although they look identical in your
output below).

If FALSE, then you just need to confirm that the species names are
actually identical (is there a space at the end of one?, or manually
re-type to confirm, etc., etc.).

Good luck,
Phil

On 7/15/2015 8:42 AM, Laura Riggi wrote:
> Dear R community,
>
>
>
> I  have some trouble with the dbFD function in the FD package.
>
>> str(a)
> 'data.frame':    150 obs. of  48 variables:
>
>> str(x)
> 'data.frame':    48 obs. of  9 variables:
>
>
>
> ex1 <- dbFD(x,a)
>
> Error in dbFD(x, a) :
>
>   Species labels in 'x' and 'a' need to be identical and ordered alphabetically (or simply in the same order).
>
>
>
> I have checked multiple time the data set but this message keeps on appearing. The names of the species are identical in both data.frames.
>
>
>
> I was wondering if you could help me by giving me an example of an excel trait and species matrix table to upload for this package. Below is a snapshop of my data. I have also checked that there are no NA's problems and that there is no species abundance = 0 or no community with 0 species.
>
>
>
> Thank you for any advice!
>
> Best
>
> Laura
>
>
>
> Species table (a)
> Agonum_assimile
>
> Agonum_dorsale
>
> Agonum_gracile
>
> Agonum_gracilipes
>
> 2
>
> 3
>
> 0
>
> 0
>
> 0
>
> 6
>
> 0
>
> 0
>
> 1
>
> 10
>
> 0
>
> 0
>
> 1
>
> 5
>
> 0
>
> 0
>
> 0
>
> 8
>
> 0
>
> 0
>
> 2
>
> 7
>
> 0
>
> 0
>
> 1
>
> 6
>
> 0
>
> 0
>
>
>
>
>
>
> Trait table(x)
>
>
> Species
>
> SizeCategoy
>
> Ecology
>
> Reproduction
>
> Diet
>
> Wing
>
> Agonum_assimile
>
> C
>
> nocturnal
>
> spring
>
> Carnivorous
>
> Brachypterous
>
> Agonum_dorsale
>
> B
>
> nocturnal
>
> spring
>
> Carnivorous
>
> Macropterous
>
> Agonum_gracile
>
> B
>
> diurnal
>
> spring
>
> Carnivorous
>
> Macropterous
>
> Agonum_gracilipes
>
> B
>
> both
>
> spring
>
> Carnivorous
>
> Macropterous
>
>
>
>
> 	[[alternative HTML version deleted]]
>
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>
>

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 Phil Novack-Gottshall
 Associate Professor
 Department of Biological Sciences
 Benedictine University
 5700 College Road 
 Lisle, IL 60532

 pnovack-gottshall at ben.edu
 Phone: 630-829-6514
 Fax: 630-829-6547
 Office: 332 Birck Hall
 Lab: 316 Birck Hall
 http://www1.ben.edu/faculty/pnovack-gottshall
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~