On 15 October 2014 07:24, Jari Oksanen <jari.oksa...@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 > _______________________________________________ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > -- Gavin Simpson, PhD [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology