Dear R users,
I am trying to analyze multivariate abundance data using the mvabund
package, but errors occur for several functions.
I created a mvabund object named faunadat consisting of 8 dependent
variables each containing 64 positive integer values (bact, fung, plant,
omn, pred, orib, meso, spring). There are 4 factors: harv, rep, depth and
lit.
I then created a formula:
>
mvform<-mvformula(faunadat~harv*rep*lit+harv*rep*depth+harv*lit*depth+rep*lit*depth)
When I try to create a mean-variance plot, I get the following error. I
have checked and all the factors are the same length as the dependent
variables.
> meanvar.plot(mvform)
Error in default.meanvar.plot.mvformula(x = x, n.vars = n.vars, var.subset
= var.subset, :
the dimensions of the variables do not match
When I fit a multivariate linear model, there is no problem. All the
following statements give the desired result.
> lm<-manylm(mvform)
> anova(lm,nBoot=500)
> plot(lm)
However, because these are count data, I am interested in fitting a
generalized linear model instead, but then I get following error:
> glm<-manyglm(mvform,family="negative.binomial")
> anova(glm,nBoot=500)
Error in XvarIn[nterms - i, varseq > i] <- 0 :
(subscript) logical subscript too long
Also, when trying to create diagnostics plots, I get the following error.
> plot(glm)
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In default.plot.manyglm(x, which = which, caption = caption, overlay =
overlay, :
You have passed an invalid number of variables 'n.vars' to be included in
the plot. All variables will be included instead.
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf
I know the manual says "The function is not yet available for manyglm
object", but on the other hand in one of the examples provided in that same
manual a residuals vs fitted values plot can be created for a manyglm
object:
> tasm.cop.nb <- manyglm(tasm.cop ~ block*treatment,
family="negative.binomial")
> plot(tasm.cop.nb)
The design is unbalanced, I'm not sure whether that is part of the problem.
Any help would be highly appreciated,
MLV.
[[alternative HTML version deleted]]
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
