The Paleontological Society

fish
Photo courtesy of the University of Colorado Museum of Natural History

 

Supplemental Materials for Quantitative Paleobiology

Author

Title

Supplemental Files

Steve C. Wang

Principles of Statistical Inference: Likelihood and the Bayesian Paradigm

R code for examples and figures

Michal Kowalewski and Phil Novack-Gottshall

Resampling Methods in Paleontology

Resampling: glossary, R code and SAS code

John Alroy

Fair Sampling of Taxonomic Richness and Unbiased Estimation of Origination and Extinction Rates

R code for shareholder quorum subsampling and rarefaction
Instructions for using this R code

Lee Hsiang Liow and James D. Nichols

Estimating Rates and Probabilities of Origination and Extinction Using Taxonomic Occurrence Data: Capture-Mark-Recapture (CMR) Approaches

Using MARK to analyze paleontological data
MARK input file 1
MARK input file 2

Tom Olszewski

Diversity Partitioning Using Shannon’s Entropy and its Relationship to Rarefaction

 

S. Kathleen Lyons and Felisa A. Smith

Using a Macroecological Approach to Study Geographic Range, Abundance and Body Size in the Fossil Record

 

Peter D. Roopnarine

Networks, Extinction and Paleocommunity Food Webs

Appendix

Mark Webster and H. David Sheets

A Practical Introduction to Landmark-based Geometric Morphometrics

Supplemental online material

Data files for single species:
Oc_n63_tps.txt
Of_n23_tps.txt
Og_n58_tps.txt
Ot_n37_tps.txt

Data files for two species:
OcOg_n121_tps.txt
OcOg_n121_GrpList

Data files for four species:
OcOgOtOf_n181_tps.txt
OcOgOtOf_n181_GrpList

Peter J. Wagner and Jonathan A. Marcot

Probabilistic Phylogenetic Inference in the Fossil Record: Current and Future Applications

 

Anjali Goswami and P. David Polly

Methods for Studying Morphological Integration and Modularity

Goswami and Polly Modularity 1.0.m

Macaca_mulata.csv

Marmota_siberica.csv

Modularity for Mathematica Users Guide 1.0

Gene Hunt and Matthew T. Carrano

Models and Methods for Analyzing Phenotypic Evolution in Lineages and Clades

Supplement: likelihood calculations and R objects
Data used in this chapter – R workspace file

Peter M. Sadler

Brute-force Biochronology: Sequencing Paleobiologic First- and Last-Appearance Events by Trial and Error

How to download CONOP
CONOP: extended course notes

Charles R. Marshall

Using Confidence Intervals to Quantify the Uncertainty in the End-points of Stratigraphic Ranges

 

 

Software Resources for Quantitative Paleobiology

General Purpose (Free)

Platform

URL

Notes

R

http://www.r-project.org/

Particularly strong for statistical methods.  Extendible with user-contributed packages.

Octave

www.gnu.org/software/octave/

Good for numerical computing; similar in capabilities to Matlab.

 

General Purpose (Commercial)

Platform

URL

Notes

Matlab

http://www.mathworks.com/

Good for numerical computing.

Mathematica

http://www.wolfram.com/

Particularly strong for symbolic math.

 

Specialized Software (Free)

Site

URL

Notes

SUNY Stony Brook Morphometrics

http://life.bio.sunysb.edu/morph/

Compilation of resources for morphometrics.

IMP

http://www3.canisius.edu/~sheets/moremorph.html

Integrated Morphometrics Package suite of programs.

Conop

See Sadler chapter supplement.

Constrained optimization for biochronology.

MARK

http://www.phidot.org/software/mark/

Capture-Mark-Recapture software.  See Liow and Nichols chapter supplement for instructions.