[R] reception of (Vegan) envfit analysis by manuscript reviewers

I'm getting lots of grief from reviewers about figures generated with the envfit function in the Vegan package. Has anyone else struggled to effectively explain this analysis? If so, can you share any helpful tips? The most recent comment I've gotten back: "What this shows is which NMDS axis separ

[R] hold position of vertices constant in network {statnet}?

I am a novice with network fuctions! I have been exploring the network function in the statnet package, but haven't been able to figure out how to hold vertices in position while varying edge features. Can anyone advise on whether this is possible, and if so, how to do it? Thanks! -- Matthew Bakke

[R] convert non-ultrametric phylo to dendrogram

I am beginning to work with the 'ape' package in R, and have run into some trouble. I generated a UPGMA tree based on DNA sequence distance in Paup* and read it into R, where it became an object of class "phylo". However, I need it to be classified as a "dendrogram" for my purposes (to use it to or

[R] ordisurf (pkg vegan) gives implausible result

I'm having trouble with the ordisurf function in the vegan package. I have created an ordination plot (cmdscale) of 60 samples based on Bray-Curtis dissimilarities, and would like to overlay various soil edaphic characteristics as possible clues to the clustering I observe in my plot. However, I f