Summarize Data by Several Variables

Here's an example how to conveniently summarize data with the cast function (package reshape). By the way you see how this could be done "in-conveniently" by hand. You also see how a for-loop works and how a matrix is constructed and filled. In addition this serves as an illustrative example how flexible "indexing" in R works, as seen in the below loop! (download data) (this example is adapted from https://stat.ethz.ch/pipermail/r-sig-ecology/2011-May/002174.html)

Bootsrap Confidence Intervals, Stratified Bootstrap

 Here's a worked example for comparing group averages with bootstrap confidence intervals and allowing for different subsample sizes by calling the strata argument within the bootstrap function.

The data (simulated) is set up analogous to an before-after impact experiment conducted on plots across 4 levels of a grouping factor ('stage'). Similarities were calculated for each composition before and after an impact and will be averaged over the grouping factor. Our hypothesis was that the levels of the grouping factor would show significantly different average similarities - that is, a higher/lower impact on composition. As plots were aggregated in different sites within the 'stages', this dependency had to be allowed for by use of the "strata" argument in the boot.ci call.

The conclusion from this simulated example would be that the averages similarities at stages C and D are significantly different from stages A and B. That is, as the similarities are higher in C and D than in A and B, impact on composition is significantly lower in C and D.

Test Difference Between Diversity-Indices of Two Samples with Abundance Data

I adapted a permutation test from the PAST Software (Hammer & Harper, http://folk.uio.no/ohammer/past/diversity.html) that tests difference between diversity-indices of two samples with abundance data in R... See the example below:

Multivariate Repeated Measurements with adonis():

Please check the updated code in the comment by Wallace Beiroz, 26 January 2015 at 13:37!

Lately I had to figure out how to do a repeated measures (or mixed effects) analysis on multivariate (species) data. Here I share code for a computation in R with the adonis function of the vegan package. Credit goes to Gavin Simpson providing most of the important pieces of the below code in R-Help.