- Chapter 1
- Chapter 2
- Chapter 3
- Chapter 4
- Chapter 5
- Chapter 6
- Chapter 7
- Chapter 8
- Chapter 9
- Chapter 10
- Chapter 11
introduction to r (SUPPLEMENTARY appendix)
FOUNDATIONAL AND APPLIED STATISTICS FOR BIOLOGISTS using r
Motivation Statisticians have complained to me at national meetings that biologists should be prevented from attempting serious statistical analyses because they often misapply procedures and misinterpret outcomes. This view, however, is unproductive. The biologist, in the ideal, is the best possible analyst of biological data because she is knowledgeable about the system to which inferences are being made.
The premise of the book is that solid statistical foundations lead to the correct application of procedures, a clear understanding of analyses, and valid inferences concerning phenomena. In my opinion this requires both an exposure to the underlying tenets of science and a consideration of foundational mathematics. This is a departure from classic biometric texts, which discuss applications without underpinnings.
Approach My approach is to encourage students to construct their own sense of what is being learned using the R computational environment. Unlike commercial statistical software R does not hide its algorithms in black boxes. Instead, complex procedures can be viewed step by step to demonstrate how results, shown in textbooks, are obtained. In addition, the superb graphical capabilities of R allow interactive demonstrations to aid in comprehension. A companion package to this book called asbio has been created specifically for this purpose.
A link to the classroom-tested document "Introduction to R" and code for all figures in the text are provided here (see left panel).
Instructors who wish to receive worked answers to selected exercises from the textbook can contact me personally.
Errors A frustrating reversal of the conditionality of P-values occurs on pages 90 and 199 although it is stated correctly elsewhere. The true conditionality is P(data|H0).
I welcome the discovery of new errors, though please verify that they are actually new by checking the errata. Instructors and students should be aware that the errata includes corrections to exercises.
A novice to command line interfaces can install and load asbio, and access the central “point and click” book menu by typing just three commands into R:
Subsequent access to the menu during new work sessions requires only the last two commands.