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 that person 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 while using R as a pedagogic facilitator. 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 R package to this book called asbio has been created mainly for this purpose.
A link to the classroom-tested document "An Amalgam of R" and code for all figures in the text are also provided here (see left panel).
Errors
In the 1st printing 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). Also, in typesetting, "equal" and other signs have been removed from figure code in a number of places. I apologize for these and other errors, and welcome the discovery of new errors. Please verify, however, that they are actually new by checking the errata. Instructors and students should be aware that the errata includes corrections to exercises. A second printing, published in the fall of 2015, corrects these and other errors.
Additional Teaching Materials
Instructors who wish to receive worked answers to selected exercises from the textbook can contact me personally. Also available are extensive knitr-generated classroom slides for Chs. 1-11 and lists of test questions.
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The asbio Package
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:
install.packages("asbio")
library(asbio)
book.menu()
Subsequent access to the menu during new work sessions requires only the last two commands. Considerations for running asbio on specific operating systems are provided below. Users for all OS variants should install the newest version of R, and asbio.
Asbio uses the package tkrplot for the implementation of some minor GUI components. In package development, an effort has been made to make the tkrplot plot "Required" by asbio, making installation unnecessary. To install tkrplot simply run install.packages("tkrplot") at the R command command line (although see description for potential Linux/Unix tkrplot issues below).
Windows
Because asbio was primarily built and tested in Windows, asbio should work well with modern implementations (≥ ver 10) of Windows OS. If required, older versions of asbio (and R), for all major operating systems, can be found at CRAN.
Linux/Unix
Linux/Unix users, for full asbio GUI functionality, please install BWidget (a set of auxiliary Tcl/Tk scripts). This can be done by running the following at a terminal:
sudo apt-get install bwidget
for Debian/Ubuntu, and for Fedora:
sudo yum install bwidget
Some minor components of asbio GUIs currently require the R package tkrplot. Unfortunately, installing tkrplot at the R command line, in Linux, is currently problematic because of (apparently) a header file issue. One can, however, install tkplot from a terminal using:
sudo apt install r-cran-tkrplot
for Debian/Ubuntu, and for Fedora:
sudo yum install r-cran-tkrplot
No other programmatic actions are currently needed.
MAC OS
Mac users, please download the most recent version of XQuartz to allow general implementation of tcltk GUIs in asbio. I strongly recommend that asbio be run from the R.app or from RStudio, and not from Mac OS R-GUI, as asbio animations are currently run incorrectly in this setting (only last plot shown).
For full asbio GUI functionality, BWidget (a set of auxiliary Tcl/Tk scripts) must be installed. This is "fairly" easy to do, and will be facilitated if you have administrative permissions at your terminal. If you need to set up a Mac OS password, follow the instructions here.
First, download and un-compress BWidget. You can do this "by hand" (i.e., manually downloading BWidget, and un-compressing its contents, for instance, using: tar xf bwidget-version.tar.gz), or using Homebrew, or some other Mac OS package manager. A self-contained package installer for Homebrew (recommended) can be found here. Homebrew, which is called from a terminal shell, will require installation of xCode command line tools. Given these preliminaries, BWidget can be installed from the terminal command line using:
brew install bwidget
The command above should automatically un-compress the BWidget tarball or .zip file, resulting in a folder, named bwidget, containing Tcl scripts, located in the Homebrew lib directory.
Second, either (a) copy or move the un-compressed bwidget directory to a place that tcltk can find it, or (b) set an environmental path to it.
Under (a) (recommended), one should attempt to copy or move the bwidget directory into an existing Tcl or tcltk auto path. To obtain existing tcltk auto paths, you can type the following in R:
strsplit(tcltk::tclvalue('auto_path'), " ")[[1]]
On my Mac Tahoe OS 26.0.1, running R-4.5.1, I get the following R output:
[1] "/opt/R/x86_64/lib/tcl8.6"
[2] "/opt/R/x86_64/lib"
[3] "./lib"
[4] "/opt/R/x86_64/lib/tk8.6"
[5] "/opt/R/x86_64/lib/tk8.6/ttk"
To copy the bwidget directory to a detectable location, you could navigate to the Homebrew lib directory, from a terminal, and run something like:
sudo cp -r bwidget /opt/R/x86_64/lib/tcl8.6
Unfortunately, your chosen directory may be unwritable.
Under alternative (b), one could set a temporary Tcl path to bwidget. Open R and specify:
tcltk::addTclPath("path/to/bwidget scripts")
For me, this is:
tcltk::addTclPath("/opt/homebrew/lib/bwidget")
Unfortunately, one will have run this code at the beginning of every R session that uses asbio GUIs that require bwidget scripts. Note that one could automate this process by creating or modifying an .Rprofile file to run the snippet every time R is opened.
Third, confirm that BWidget is working. Load asbio in R and run:
see.pdfdriver.tck()
If BWidget scripts are inaccessible, this code will produce an error.