UGA Stratigraphy Lab

The data is in the strata

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. Macintosh programs for OS X (blue X icon) are saved as .zip files; those for pre-OS X systems (happy mac icon) are saved as binhex files, which can be opened with Stuffit Expander. If you have any comments or questions, please contact Steven Holland at stratum@uga.edu.

Biostrat 1.7

Biostrat 1.7 is a model for the stratigraphic distribution of fossils within depositional sequences. It is an extension of the models used in Holland (1995a), Holland (1995b), and Holland and Patzkowsky (1997a). This is the most recent version and is capable of handling files produced by STRATA. Setting up STRATA to produce water depth files for Biostrat 1.7 requires special instructions. Biostrat 1.7 comes with instructions.

Note: Biostrat 1.7 is not compatible with OS X 10.6 (Snow Leopard)

Rarefaction

I have two programs for doing rarefaction calculations. The first is based on the analytic solution presented by Raup (1975) and Tipper (1977) and runs very quickly, even on large data sets. The second is based on a resampling routine and can be used to cross-check the analytic calculations, but runs much slower than the analytic solution. Be sure to read the instructions for Analytic Rarefaction.

 

Analytic Rarefaction

Resampling Rarefaction

Percentage Error Bars

This 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. At present, there is no readme file for this program. 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" for source code on which this program is based and for a justification of the approach used in calculating these error bars.

Backstripping

This 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. Backstripping comes with instructions.

Cross-correlation

This program is used to correlate meter-scale cycles from two outcrops. One section should be longer than the other. The long section is also assumed to totally contain the stratigraphic interval of the shorter; this can be checked with distinctive marker beds, etc. The program will first read a text file you prepare that lists the thicknesses of successive meter-scale cycles in one section, and then will read the thicknesses of the cycles in the other section from another file. The program will then calculate the correlation coefficient of all possible correlations between the two sections and will also calculate confidence levels on the correlation coefficient, based on resampling of the cycles actually measured. Cross-correlation comes with instructions.

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 course in Data Analysis covers a variety of topics in statistics and data analysis, and it emphasizes how to use R to solve these problems.

Using BBEdit as your R editor

You can use BBEdit, the powerful text editor for OS X, 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 Mac OS X, I recommend this course by Aaron Hillegass. Read my review.