Software
I have written several programs that are available free of charge. All I ask is that if you use these for research that results in a presentation or published paper, acknowledge me. Most of these (except for Analytic Rarefaction) are available only for macOS. If you have any comments or questions, please contact Steven Holland at stratum@uga.edu.
 |
Analytic RarefactionAnalytic Rarefaction uses the solution presented by Raup (1975) and Tipper (1977) and runs very quickly, even on large data sets. Be sure to read the instructions for Analytic Rarefaction. |
 |
Margin of ErrorThis program is based on David Raup’s program for calculating the error bars on percentage or ratio data that he presented in the 1991 Analytic Paleobiology short course. For source code on which this program is based and a justification of the approach used in calculating these error bars, see Raup, D.M., 1991, The future of analytical paleobiology. In N.L. Gilinsky and P.W. Signor, eds., Analytical Paleobiology, Paleontological Society Short Courses in Paleontology No. 4, p. 207–216. |
 |
BackstripThis program is used to make backstripping calculations for a single section. The program assumes local isostasy, makes compaction corrections using the coefficients found in Sahagian and Holland (1991: Geology 19: 1209–1212), and integrates compaction corrections over the thickness of a unit, resulting in more accurate decompaction of thick units. |
R tutorials
If you need a jump-start in using R or in using multivariate methods in R, try these tutorials, which should get you up and running quickly.
R tutorial
Cluster analysis tutorial
Principal components analysis tutorial, with accompanying data set
Detrended correspondence analysis tutorial
Non-metric multidimensional scaling tutorial
The website for my graduate-level course Data Analysis in the Geosciences, which covers a variety of topics in statistics and data analysis, and it emphasizes how to use R to solve these problems.
Installing sedflux on macOS
Installing sedflux can be tricky, and these steps will install it in just a few minutes.
Using BBEdit as your R editor
You can use BBEdit, the powerful text editor for macOS, as your editor for R, including syntax highlighting. To specify BBEdit as your external editor, go to the R application menu, select Preferences, then choose Editor (under Source Editor). Click the External Editor button on the top right, then click the New editor button. In the dialog that appears, scroll to BBEdit and either double-click it, or click it once and click the Open button. When you return to the preferences panel, be sure the radio button for Application is selected, rather than the Command button. Close preferences.
Now, when you create a new document in R, either from the File menu or from the toolbar, BBEdit will automatically open. To have BBEdit automatically launch when you double-click a .R file, and to have BBEdit have syntax coloring, you’ll need to do a couple more steps.
First, download the syntax-coloring file, uncompress the Rplist.zip file that is downloaded, and copy the R.plist file to the ~/Library/Application Support/BBEdit/Language Modules/folder (this is the Library folder in your user folder, not the Library folder at the root level of your system). If the Language Modules folder isn’t present, go ahead and make one, and put the R.plist file inside of it. Quit BBEdit and relaunch it. When you double-click a file with a .R suffix, BBEdit should launch and display your code with syntax highlighting. If you create a new document from within R, you’ll need to tell BBEdit that this is an R file in one of two ways: 1) Save the file with .R suffix, or 2) go to the bottom of the window, click the two arrows that display a list of computer languages, and select R from the list.
Cocoa Bootcamp at the Big Nerd Ranch
If you’re interested in developing software for macOS, I recommend this course highly. Read my review. of when I took the course.
