Supplemental Materials for Quantitative Paleobiology

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.