Dear all, I am using distance-based RDA in vegan 2.4-1 with direct decomposition (no constant added, imaginary axes included) and trying to test axis significance. Permutations seem to work with first=FALSE, but not first=TRUE. The error message is "invalid comparison with complex values".
Here is my code: library(vegan) data(pyrifos) ditch <- gl(12, 1, length=132) week <- gl(11, 12, labels=c(-4, -1, 0.1, 1, 2, 4, 8, 12, 15, 19, 24)) dose <- factor(rep(c(0.1, 0, 0, 0.9, 0, 44, 6, 0.1, 44, 0.9, 0, 6), 11)) res_rda_pyrifos_inv_BC<-dbrda(pyrifos~interaction(week,dose) + Condition(week), distance = "bray") ctrl_pyrifos <- how(plots = Plots(strata = ditch,type = "free"), within = Within(type = "series"), nperm = 99) permutest(res_rda_pyrifos_inv_BC, permutations=ctrl_pyrifos, first=TRUE) I get this message: "Permutation test for dbrda Plots: ditch, plot permutation: free Permutation: series Number of permutations: 9999 Call: dbrda(formula = pyrifos_inv_raw ~ interaction(week, dose) + Condition(week), distance = "bray") Error in x$F.perm >= x$F.0 - EPS : invalid comparison with complex values" Any help would be appreciated! Thanks, Cleo Tebby ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
