Software using R

These programs perform various types of morphometric analyses using R, a free software environment for statistical computing and graphics.

Momocs aims to provide a complete and convenient toolkit for morphometrics. It is intended for scientists interested in describing quantitatively the shape, and its (co)variations, of the objects they study. Detailed description.

Install the devtools package from my GitHub repository. Contributed by Vincent Bonhomme.

Morpho provides a rich toolset for Geometric Morphometrics and mesh processing in R. This includes (among other stuff) mesh deformations based on reference points, permutation tests, detection of outliers, processing of sliding semi-landmarks, im- and export of a variety of triangular surface mesh files. Download the version suitable for your OS from CRAN. Contributed by Stefan Schlager.

A morphometrics package in R for the collection and analysis of landmark-based geometric morphometric data. It is available on the CRAN package website. Thanks to Dean Adams.

R function to read .TPS files into R data frames. Thanks to Ananda Mahto (mrdwab).

Analysis of Ecological Data : Exploratory and Euclidean methods in Environmental sciences. Contains commands for Procrustes fitting. Daniel Chessel, Anne-Beatrice Dufour and Stephane Dray, with contributions from Jean R. Lobry, Sebastien Ollier, Sandrine Pavoine and Jean Thioulouse.

The function attaches the dorsal and ventral aspects of the skull, or any other two aspects of the same structure, based on common landmarks. Applicable to both 2D and 3D. Developed by Annat Haber (University of Chicago).

The function uses object symmetry to find the symmetry plane following Klingenberg et al. 2002 (Evolution 56:1909-1920) and fills in missing lateral landmarks by reflecting from the other side. Applicable to both 2D and 3D. Developed by Annat Haber (University of Chicago).

The function aligns the specimen along the midline plane based on the midline landmarks. It has the option of filling in missing lateral landmarks by reflecting from the other side, and averaging the left and right sides. Applicable to both 2D and 3D. Developed by Annat Haber (University of Chicago).

The shapes package is a set of procedures for statistical shape analysis in R. Includes functions for Bookstein baseline registration for 2D data, GPA for 2 and higher dimensional data, plotting of shapes, and other functions. Index file listing the main functions. By Ian Dryden. Version 1.0-7.