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This book is a decent introduction to statistical modelling with R. It contains clear and useful information about how to perform analysis, with guidance in both statistical interpretation and R programming. It outlines pitfalls such as over-dispersion, and clearly explains the meaning of the model results (coefficients, depending on the analysis).
Review: Statistics: An Introduction Using RUser Review - Damian Satterthwaite-Phillips - Goodreads
Better as an intro to R than as an intro to stats, but if you already have a reasonable stats background, this book is great. Read full review
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Professor Mick Crawley -- Department of Biological Sciences