(This article was first published on Software for Exploratory Data Analysis and Statistical Modelling, and kindly contributed to R-bloggers)
R can be used to perform various matrix calculations. This include functions for creating matrices (matrix), addition (+), multiplication (%*%) and inversion (solve).

Fast Tube by Casper
Other useful resources are provided on the Supplementary Material page.
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Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).