Good Morning, first let me thank you very much for answering my first two questions on this list.
Currently, i do vegan's EnvFit to simple PCA ordinations. When drawing the biplot, one can set a cutoff to just fit the parameters with significant p-values (via p.max=0.05 in the plot command). There is already sufficient coverage on the net for biplotting this kind of data with ggplot2 (with the problem being the arrow length). http://stackoverflow.com/questions/14711470/plotting-envfit-vectors-vegan-package-in-ggplot2 However, what the solution is not covering is the exclusion from insignificant environmental parameters, as the score extraction process as described in the link only works with 'display="vectors"': |Envfit_scores<- as.data.frame(scores(list_from_envfit, display= "vectors")) |||| | envfit creates lists like this: PC1 PC2 r2 Pr(>r) param1 -0.70882 0.70539 0.0994 0.000999 *** param2 -0.60122 0.79908 0.0593 0.000999 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 P values based on 999 permutations. The list contains a vector called $pval containing the pvalues. So, i need to reduce the list created by envfit to rows meeting a criterion in $pval (via "unlist" and "which", i suppose). However, i have difficulties to work out the correct code. Any help is much appreciated! -- Tim Richter-Heitmann (M.Sc.) PhD Candidate International Max-Planck Research School for Marine Microbiology University of Bremen Microbial Ecophysiology Group (AG Friedrich) FB02 - Biologie/Chemie Leobener Straße (NW2 A2130) D-28359 Bremen Tel.: 0049(0)421 218-63062 Fax: 0049(0)421 218-63069 [[alternative HTML version deleted]]
______________________________________________ R-help@r-project.org mailing list 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.
