[R] PCA scores and loadings

Dear R users group I have performed PCA using the function rda in vegan and then used plot(pcaobject). I have a couple of questions: 1) The default plot shows the individual sites (black) and the variables (red). What I want however is a plot showing the mean of site groups with bidirectiona

[R] Identification of variables contributing to differences between factor in adonis

Dear all I have used permutational multivariate analysis of variance (adonis in package vegan) based on Bray-Curtis distances to assess the signifance of carbon, nitrogen and more complex nutrient amendments on soil microbial community structure (microbial fatty acids). I have identified sig

[R] PCA or CA

Dear all I have a data set for which PCA based between group analysis (BGA) gives significant results but CA-BGA does not. I am having difficulty finding a reliable method for deciding which ordination technique is most appropriate. I have been told to do a 1 table CA and if the 1st axis is>