search for: permu

...R-experts, I am using the envfit function over an ordination of floristic data. The problem is that every time that I run it changes the results. Sometimes dramatically, selecting variables that the first time were not significant. I do not get what could be the problem or if is normal given the permutations are different. # the NMDS ordination gap_flor_NMDS_chord <- metaMDS(gaps_flor, distance = "euclid", k = 2, trymax = 20, autotransform =TRUE, noshare = 0.1, wascores = TRUE, expand = TRUE, trace = 1, plot = FALSE, old.wa = FALSE, zerodist = "add") # the environmenta...

Hi R experts, I'm looking for some help with plotting vectors from envfit in vegan, onto a 3d plot using ordiplot3d. So far I have data.mds <- metaMDS(data, k=3,trace = FALSE) vect_data<-envfit(data.mds,vegdata[,3:21],choices=1:3,permu=9999) ordiplot3d(data.mds,envfit=vect_data) ordixyplot(data.mds,pch=pts,envfit=vect_data) (my data's not really called data, I thought it might be easier to communicate this way) These display the vectors as arrows, but what I would really like is for the arrows to be labelled, like what come...

Hello there, I'm trying to plot vectors with p<0.1 in a NMDS ordination plot using p.max. Below the scripts I'm using. I guess I'm missing something! could you please give me a hand? species<-metaMDS(species_matrix)ef<-envfit(species,environmentaldata_file,permu=999,na.rm=TRUE)efplot(species, dis="sites")plot(ef,p.max=0.1) Error in plot.envfit(ef, p.max = 0.1) : (subscript) logical subscript too long Many thanks! Laura [[alternative HTML version deleted]]

...olAuton, SScomp [,14:19], distance = "euclidean", add = TRUE) ### NOTE: pseudo-F values are the same with or without correcting for negative eigenvalues (although they are different from other programs). ## Sequential test for terms anova.cca(m1, by="terms", perm.max=1000, permu=500) Thank you very much for any help or insights that anyone can provide, Kristen Kristen A. Ross, PhD Post Doctoral Researcher University of Illinois at Chicago kristenrossUIC@gmail.com and Research Associate Green Mountain College One Brennan Circle Poultney, VT 0576...