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| Preface | |
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| What this book is about | |
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| What you need to know to make this book work for you | |
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| How the book is organized | |
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| Why R? | |
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| Import, Explore, Graph I-Getting Started | |
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| Where to put your data | |
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| Make a folder for your instructions (code, script) | |
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| How to get your data into R and where it is stored in R's brain | |
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| Working with R-hints for a successful first (and more) interaction | |
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| Make your first script file | |
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| Starting to control R | |
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| Making R work for you-developing a workflow | |
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| And finally … | |
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| Import, Explore, Graph II-Importing and Exploring | |
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| Getting your data into R | |
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| Checking that your data is your data | |
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| Summarizing your data-quick version | |
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| How to isolate, find, and grab parts of your data-I | |
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| How to isolate, find, and grab parts of your data-II | |
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| Aggregation and how to use a help file | |
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| What your first script might look like (what you should now know) | |
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| Import, Explore, Graph III-Graphs | |
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| The first step in data analysis-making a picture | |
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| Making a picture-bar graphs | |
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| Pimp my barplot | |
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| Making a picture-scatterplots | |
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| Pimp my scatterplot: axis labels | |
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| Pimp my scatterplot: points | |
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| Pimp my scatterplot: colours (and groups) | |
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| Pimp my scatterplot: legend | |
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| Plotting extras: pdfs, layout, and the lattice package | |
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| Doing your Statistics in R-Getting Started | |
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| Chi-square | |
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| Two sample t-test | |
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| The first step: plot your data | |
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| The two sample t-test analysis | |
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| General linear models | |
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| Always start with a picture | |
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| Potential statistical and biological hypotheses-it's all about lines | |
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| Specifying the model | |
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| Plot, model, then assumptions | |
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| Interpretation | |
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| Treatment contrasts and coefficients | |
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| Interpretation | |
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| Making a publication quality figure | |
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| Coefficients, lines, and lines() | |
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| Expanded grids, prediction, and a more generic model plotting method | |
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| The final picture | |
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| An analysis workflow | |
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| Final Comments and Encouragement | |
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| Appendix: References and Datasets | |
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| Index | |