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Index
Preface How to use this book Acknowledgements Chapter 1: A first R session
What is R? A first R session
Chapter 2: Basics
Commands, objects and functions Functions Vectors, Matrices and Data Frames Data types and Data frames Choosing data: subscripts and subsetting Packages
Chapter 3: Importing Data and Record Keeping
Importing Data Record Keeping Script Editors What to Save
Chapter 4: Decrypting the Help Files and Error Messages
Using the help files Error messages and other problems
Chapter 5: Graphs
Scatterplots Drawing curves Plots of Variables by Factors Using transparency in your graphs More Graphics Functions Exporting Graphics Going Further with your Graphs Exercises
Chapter 6: Basic Statistical Concepts
Populations and Samples Descriptive and exploratory statistics Standard errors and confidence intervals
Chapter 7: What is statistical testing?
The problem Statistical testing in a nutshell How a statistical test works What statistical testing does and doesn't tell us
Chapter 8: The Chi-squared Test and a Classic Dataset on Smoking and Cancer
Are lung cancer patients who smoke more likely to be heavy smokers? Are lung cancer patients more likely to be smokers than the controls?
Chapter 9: Comparing immune responses between two caterpillar species using a t-test
Assumptions and limitations of standard parametric statistics Importing the Data Descriptives and Initial Exploration Comparing Two Means With a t-test
Chapter 10: Correlation analysis Chapter 11: Using Linear Regression to Analyse TB trends in the UK
Bovine TB Multi-drug resistant TB Footnotes
Chapter 12: Yeast Sex and ANOVA
Analysis of Variance Yeast sexual selection Understanding the coefficients table Which statistical tests to use with lm()? Diagnostics Visualising the data
Chapter 13: General Linear Models, Whale Brains and Dive Duration
Whale brains and dive duration
Chapter 14: Basic programming in R
Writing scripts using a text editor Writing functions Exercises
Chapter 15: Vector and matrix operations
See also… See also also… Exercises
Chapter 16: Loops
Writing a mathematical model using a for() loop Other useful loops Exercises Footnotes
Chapter 17: Conditional statements
Exercises
Chapter 18: Coding and Optimising Conway's Game of Life Chapter 19: An Interactive Line Fitting Function
Writing our function: planning Module 1: user input of the wells to be analysed Module 2: user input for the regression line for each well and fitting the regression Module 3: assembling the output The finished function
Appendix 1: R colour names Appendix 2: R Resources
Statistics Searching for information Books on the basic uses of R Books on statistical analysis in R Books on R graphics Books on R programming Videos Websites Mailing lists
Appendix 3: Smiley faces and rainbows Appendix 4: Solutions to exercises
Chapter 2: Basics Chapter 5: Graphics Chapter 14: Basic Programming Chapter 15: Vector and Matrix Operations Chapter 16: Loops Chapter 17: Conditionals
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