From Bolker’s glmmFAQ
A good walkthrough
Websites / Blogs
SAMPLE(ECOLOGY): NMDS TUTORIAL IN R (blog)
Below are some blogs related to the question of interactions in ANOVA. They might not be super-accessible for ‘yins – they are mostly discussions among well practiced stats users and not attempts to explain the issue in general terms. One thing I think is apparent though is that I think the problem is not well defined – when someone says “how do you interpret interactions” different people think of it in terms of experiments analyzed with an ANOVA with only categorical variables, while others think in terms of regression with interactions between two continuous variables, or between a continuous and categorical variable. I also think some people think in terms of how you interpret the result of an ANOVA table (which basically just tells you p-values) and interpretation of the means and other parameters you can get from your model.
Dynamic Ecology: Interpreting ANOVA interactions and model selection: a summary of current practices and some recommendations (also see the comments on their Poll: How do you interpret two-way ANOVAs?)
Andrew Gelman: Main effects and interactions
This mentions the ade4 package, and factominer
The factorminer package also does mca
I think this is the reference that might be the origin of PCA w/ categorical variables in ecology related fields
Hill & Smith 1976 Principal component analysis of taxonomic data with multistate discrete characters
The package ade4 has a function dudi.mca() for multiple correspondence analysis (PCA w/categorical variables) and dudi.hillsmith() which allows you to do a mix; its probably similar to that PCAmix package I sent. ade4 is part of a suite of packages by crazy French ecologists that are REALLY into multivariate stuff- I find most of the documentation really hard to understand (lots of math, not much ecology, not perfect English). They have a paper “The ade4 package: implementing the duality diagram for ecologists” In the Journal for Statistical Software which has a section “4. An example: dudi.hillsmith” where they analyze the “dune meadow” dataset that shows up often in vegan I think. This example, whether analyzed with dudi.hillmsith or the functions in the PCAmix package (or whatever its name is) might be a good place to start.
ONE MORE TIME: NWO, GENDER BIAS AND SIMPSON’S PARADOX
Dutch sexism study comes under files
Simpson’s paradox visualization