[R-sig-eco] Error in CAPdiscrim() in BiodiversityR

[Jari Oksanen]

On 13/02/2012, at 20:23 PM, Edgar Torres wrote:

> Hello everyone,
> 
> 
> I am using CAPdiscrim function, but when I try to do the ordiplot it sends me an error message:
> 
> Erreur dans scores.default(ord, choices = choices, display = "sites") :   indice hors limites (French)
> Error in scores.default(ord, choices = choices, display = "sites") : index out of range (English)
> 
> 
> I use a data frame where columns are species and rows are sites. And I have a data frame with "environmental" variables, but my interest is to compare between two sampling periods. As I have my data they work when I use adonis and/or betadisper functions in vegan, my code is very similar to that in the CAPdiscrim help.
> During each sampling period I have different sample size. May this affect the test?
> 
> Ordi <- CAPdiscrim(x1 ~ Prog, data=s1, dist="bray", axes=4, m=0, permutations=99)
> p1 <- ordiplot(Ordi)
> 
> ordisymbol(p1, s1, "Prog", legend=F)
> 
> where x1 is the abundance data frame and Prog is the factor for sampling periods.
> 
> When I see the results of Ordi I find only a vector of LD, and when I do the analysis with dune data there are two vectors
> 
> $x
>                                                                        
> LD1
> 3_108                                                             0.07802716
> 3_120                                                             1.39745127
> 3_137                                                             0.23724478
> 3_143                                                            -1.56716987
> 
> 
> Do you have any idea about this error?

So what is the error?

Cheers, Jari Oksanen

-- 
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
jari.oksanen at oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa