search for: oecosimu

...using vegan package (R version 2.11) trying to calculate checkerboard units for each species pair of a matrix. I've prepared the function: pair.checker=function (dataset) {designdist (dataset, method="c("(A-J)x(B-J)", terms ="binary", abcd=FALSE)} to use with function oecosimu as follows: oecosimu(dataset, pair.checker, "tswap", nsimul=5000, burnin=0, thin=thin, statistic="pair.checker") It seemed to work but the output did not include each species pair name. I don't know what to do. First column was all NAs. I copied and pasted the results of t...

I am currently testing species co-occurrence patterns using null models and the oecosimu() function within the vegan() package. My issue is that none of the methods appear to be the ones that I want. The methods listed are r0, r1, r2, r2dtable, swap, tswap. However, I want to know how to go about implementing fixed row algorithms, as suggested in Gotelli 2000 in Ecology. Also, the nu...

....com/vegandevs/vegan/issues/36 . Currently the following functions can use parallel processing: adonis, anosim, anova.cca, mantel, mantel.partial, mrpp and simper can use it permutations, bioenv can asses several competing models in parallel, metaMDS can launch several random starts in parallel and oecosimu can use parallel processing in evaluating the statistics for null communities. If you compare this to the previous list of permutation functions, you see that the following permutation methods do not use parallel procesing: CCorA, envfit, mso, permutest.betadisper and protest. The question is if th...