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“Statistics with R” is a great R graphics & stats website. It provides lots of R examples, covering many analytics topics. It is also available as a PDF document to download at the website, as well as the R codes. The table of contents of the document are as below.

1. Introduction to R
2. Programming in R
3. From Data to Graphics
4. Customizing graphics
5. Factorial methods: Around Principal Component Analysis (PCA)
6. Clustering
7. Probability Distributions
8. Estimators and Statistical Tests
9. Regression
10. Other regressions
11. Regression Problems — and their Solutions
12. Generalized Linear Models: logistic regression, Poisson regression, etc.
13. Analysis of Variance (Anova)
14. Mixed Models
15. Time series
16. Miscellaneous
17. Applications