[R-sig-eco] SIMPER problem: invalid 'nrow' value (too large or NA)

[Gavin Simpson]

On 15 October 2014 07:24, Jari Oksanen <jari.oksanen at oulu.fi> wrote:

>
> On 14/10/2014, at 21:41 PM, mastratton wrote:
>
> > markusvlindh wrote
> >> Dear all,
> >>
> >> I'm having difficulty applying a SIMPER analysis found in vegan,
> following
> >> the example provided i the help function of simper. I keep receiving the
> >> following error message:
> >>
> >> Error in matrix(ncol = P, nrow = n.a * n.b) :
> >>  invalid 'nrow' value (too large or NA)
> >>
> >> My data consist of a community matrix with 200 species and 43 dates
> (class
> >> = "data.frame") and my groups consists of factors with in total 12
> levels.
> >>
> >> A mock example could be the following that is working! :
> >> library(vegan)
> >> community<-data.frame(replicate(43,sample(0:1000,200,rep=TRUE)))
> >>
> groups<-as.factor(replicate(1,sample(c("Alpha","Beta","Gamma","Epsilon","Bact","Actino","Verr","Unclass","Cyano","Plancto","Eury","Chloro"),200,rep=T))
> >> simper_test<-simper(community,groups)
> >> summary(simper_test)
> >>
> >> But please see the attached files for true data that is not working.
> >>
> >> Could someone please please assist in what is the problem with my data.
> >>
> >> Kind regards!
> >
> > Markus,
> >
> > I was getting the same error message and discovered that simper() is not
> > written to handle an input 'group' factor that has one or more unique
> values
> > with only one occurrence. Your data (reattached) have two of these
> > instances:.
> >
> ...
> > The source code for simper() can be modified to allow these instances:
> >
> Yes, the source can be modified *and* it has been modified to cope with
> one-member groups. You can install the modified version of vegan for
> Windows, or if you have programming tools for other OS's, too, using:
>
> install.packages("vegan", repos="http://R-Forge.R-project.org")
>
> This is development version, but we are going to release new CRAN version
> of vegan later this month, and the R-Forge version is very close to the
> release version. (Looks like the build system is down again in R-Forge, and
> has been for a week, so that this is not the most recent and stable version
> of R-Forge, but it is mostly safe.)
>
> Cheers, Jari Oksanen
>
>
and if you want something really up-to-date, then we do have binary builds
on Windows courtesy of the Appveyor continuous integration service.
https://ci.appveyor.com/project/gavinsimpson/vegan and click on the
artefacts tab.

G


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-- 
Gavin Simpson, PhD

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