Quantitative Methods for the Palaeobiologist
This section is meant to provide links to free programmes, which I use (and recommend) for the study of variation, phylogenetics, and macroevolution.
This section will be continuously updated.
R - The R-Project started in the early 90s and has quickly become one of the most useful and powerful programmes for statistics and graphics generation. It has a steep learning curve, but I would highly recommend any student of palaeobiology (and biology in general) to become familiar with its basic workings. Also, its free!
NB. If you decide to use R, and particularly if you are using it through a Windows-based platform, I recommend using it through RStudio. Better user interface...in my opinion.
For links associated with the basic R workshop I run at Uppsala University, click here
Personal R Packages*
MASSTIMATE (current vers. 1.3) - Body Mass Estimation Equations for Vertebrates. This package was developed to easily estimate body masses of vertebrates based on skeletal measurements. Various equations are presented, including those of Campione & Evans (2012, BMC Biology) for quadrupeds, Campione et al. (2014), for bipeds, and Campione (2017, Paleobiology).
Personal R Scripts*
(right-click to download, open script file in order to see argument details)
Linear Statistics/Plot for Multiple Groups
Intercept Comparisons @ x≠0 Using a t-test
Confidence & Prediction Intervals
Minimum Convex Hulls
Standard Error of the Estimate
Standard Parametric Tests for Multivariate Statistics
*please contact me if you find any errors or inconsistencies.
Useful R Packages
ape - Analysis of Phylogenetics and Evolution. One of the most comprehensive packages for look at evolutionary trees in R. This package is required for visualizing trees, tree manipulation, branch length calculation, independent contrasts, calculation of phylogenetic structure for generalized least squares models ('gls'), ancestral state reconstructions, character/tree simulations, and many other useful tools.
fossil - Palaeoecological and Palaeogeographical Analysis Tools. Developed by one of my closest colleagues (Matthew Vavrek), this package is meant to provide the necessary tools for ecological and biogeographic analyses, in particular from a palaeontological perspective. Tools include, among others, species richness estimation, calculation of beta diversity, and species-area plot generation.
geiger - Analysis of Evolutionary Diversification. Probably the most useful package for macroevolutionary analyses! This package was originally created by Luke Harmon, but now includes contributions from a star-studded cast of evolutionary biologists. This package includes functions to calculate diversification rates, examine disparity through time, and investigate evolutionary models for comparative data on a tree, among many others. Also, 'treedata' will match your dataset to you tree, so as to avoid mismatching errors.
geomorph - see Morphometrics Programmes
LOST - Missing Morphometric Data Simulation and Estimation. Missing data in morphometric analyses of fossils is unavoidable, but should net detract from running such analyses. This package allows one to degrade a complete dataset to test the effects of missing data, calculate the proportion of missing data in a dataset, and estimate missing data for both linear and geometric morphometrics analyses. See also.
paleotree - Paleontological and Phylogenetic Analyses of Evolution. An important package for the palaeobiologist interested in integrating fossil taxa into phylogenies. This package allows one to scale phylogenies to time (i.e., time-calibrate; partly built on Graeme Lloyd's code) and plot trees with respect to character evolution. Many other tools are also offered, including simulation of fossil datasets and diversity curve generation.
shapes - see Morphometrics Programmes
If you are interested in phylogenetics in R, I recommend you join the the R-Phylo-Sig mailing list.
TPS Suite - A series of programmes created by James Rohlf (yes, one of the authors of Biometry) that allows the digitization and analysis of landmarks and outlines (sliding semi-landmarks). This site also provides links to other morphometric programmes. The three principal programmes required for running a standard geometric morphometric analysis are: 'tpsUtil' for generating and converting file-types; 'tpsDig' for digitising specimens (landmarks and semi-landmarks); and 'tpsRelw' for running the Relative Warp (or PCA) analysis of the landmarks.
Morphometrics in R
geomorph - Geometric Morphometric Analysis of 2d/3d Landmark Data. See also geomorph.net.
shapes - Statistical Shape Analysis.