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error message in package "FD", function dbFD ()

4 messages · Laura Riggi, Sarah Goslee, Phil Novack-Gottshall +1 more

Original
Laura Riggi
# 
Dear R community,



I  have some trouble with the dbFD function in the FD package.
'data.frame':    150 obs. of  48 variables:
'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
Sarah Goslee
# 
I *think* your problem is contained in the help for ?FD, where it says
that for a, rows are sites and species are columns.

But you posted in HTML, and didn't use dput() to provide data, so your
example is hopelessly mangled.

Without a reproducible example that includes some sample data (fake is
fine), the code you used, and some clear idea of what output you
expect, it's impossible to figure out exactly how to help you. Here
are some suggestions for creating a good reproducible example:
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example

Sarah
On Wed, Jul 15, 2015 at 9:35 AM, Laura Riggi <laura.riggi at slu.se> wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Phil Novack-Gottshall
    

    

      
      #
    

  


  

      
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:

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Krzysztof Sakrejda
    

    

      
      #
    

  


  

      
2015-07-15 10:12 GMT-04:00 Novack-Gottshall, Philip M. <
pnovack-gottshall at ben.edu>:

            

      
      
      
    

        
Try the following to confirm:

            

      
      
      
    

        
Or just find the culprit directly:

row.names(x)[!(row.names(x) %in% row.names(t(a)))]
row.names(t(a))[!(row.names(t(a)) %in% row.names(x))]