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?
Thanks a lot
 
Best regards
 
EDGAR

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