GeometricMorphometricsMix

Miscellaneous geometric morphometric functions

This package provides a diverse set of functions for geometric morphometric analyses, including shape integration, disparity, association, and more. It is designed for researchers, students, and practitioners in geometric morphometrics.

Originally developed as a resource for students in the Geometric Morphometrics course (Physalia Courses), these functions have been complemented over the years with many new functions, and are now distributed as an R package for broader accessibility and ease of use.

Installation

From Github, using devtools

library(devtools)
install_github("fruciano/GeometricMorphometricsMix", build_vignettes=TRUE)

Citation

Currently, there is no formal publication describing the package (but this may be available in the future). Please, use citation() to identify the most appropriate current citation of GeometricMorphometricsMix. Importantly, each function provides reasonable comments and references to the methods, which can (and should) be used when using the functions in the package (in addition to the usual citation to the package itself).

Documentation and Help

Each function in the package is documented with usage examples and references.

Currently available functions

• adjRand_test : Permutation test of the adjusted Rand index, which quantifies the agreement between two partitions (e.g., classification of specimens obtained using different methods)
• BTailTest : Comparison of disparity between two groups
• critical_angle : Critical angle for the test of difference between two vectors
• disparity_resample : Obtain resampling estimates (bootstrap or rarefaction) of disparity statistics
• disparity_test : Comparison of disparity between two groups
• dist_mean_boot : Bootstrap estimates of the distance between group means
• EscoufierRV : Computation of Escoufier RV, which quantifies levels of association between blocks of variables (Escoufier 1973 - Biometrics)
• Kmultparallel : Parallelised computation of Adams' Kmult (useful for distributions of trees, see Fruciano et al. 2017 - Ecology and Evolution)
• LM_relativepos_check : Check relative position of landmarks, comparing it to a reference specimen (useful to identify switched landmarks and similar in raw data)
• parallel_analysis : Perform parallel analysis (useful to choose a number of principal components for dimensionality reduction)
• pls : Perform partial least squares (PLS) analysis
• pls_major_axis : For a partial least squares (PLS) analysis, compute the major axis of PLS scores, project data onto the axis and compute predicted shapes for the major axis scores thus obtained.
• ProjectOrthogonal : Projects data to subspace orthogonal to a given vector (for use in allometric correction, see Burnaby 1966 - Biometrics; Rohlf & Bookstein 1987 - Systematic Zoology; for use in dealing with measurement error, see Valentin et al. 2008 - Journal of Fish Biology; Fruciano 2016 - Development Genes and Evolution)
• rescale_by_landmark_distance : Convenience function to rescale configurations of landmarks based on a vector of inter-landmark distances
• reversePCA : Simple function to obtain the original variables (e.g., shape) from PC scores (and mean)
• rotate_landmarks: Apply a user-defined rotation of a landmark configuration about the origin
• rarefied_convex_hull : Computation of rarefied estimates of n-dimensional convex hull volume (a measure of disparity/morphospace occupation) - deprecated
• rarefied_disparity : Rarefied estimates of some measures of disparity/morphospace occupation - deprecated
• repeated_measures_test : Test of difference between two repeated measures
• RVrarefied : Computation of rarefied estimates of Escoufier RV (see Fruciano et al. 2013 - Plos One)
• RVcomparison : Permutation test for the difference in Escoufier RV (see Fruciano et al. 2013 - Plos One)
• scaled_variance_of_eigenvalues : Compute estimates of the scaled variance of eigenvalues (a commonly used measure of integration)
• TestOfAngle : Test of angle between two vectors, optionally allowing "flipping" of one of the two

Function Groups by Analysis Type

Analysis Type	Functions	Description
Analysis of Disparity	BTailTest	Traditional comparison of disparity between two groups
	disparity_resample	Resampling estimates of disparity
	disparity_test	Comparison of disparity between two groups
	rarefied_convex_hull	Computation of rarefied estimates of n-dimensional convex hull volume (measure of disparity/morphospace occupation) - deprecated
	rarefied_disparity	Rarefied estimates of various measures of disparity/morphospace occupation - deprecated
Integration/Association/Modularity	EscoufierRV	Computation of Escoufier RV coefficient, quantifying association between blocks of variables
	RVrarefied	Computation of rarefied estimates of Escoufier RV to account for sample size
	RVcomparison	Permutation test for the difference in Escoufier RV between datasets
	scaled_variance_of_eigenvalues	Compute estimates of the scaled variance of eigenvalues (measure of integration)
	pls	Perform partial least squares (PLS) analysis for covariation between blocks
	pls_major_axis	Compute major axis of PLS scores and predicted shapes along this axis
Vector/Angle Analysis	critical_angle	Critical angle for the test of difference between two vectors
	TestOfAngle	Test of angle between two vectors, with optional "flipping" of one vector
Group Comparison and Classification	adjRand_test	Permutation test of the adjusted Rand index, quantifying agreement between two partitions
	dist_mean_boot	Bootstrap estimates of the distance between group means
	repeated_measures_test	Test of difference between two repeated measures
Data Transformation and Manipulation	ProjectOrthogonal	Projects data to subspace orthogonal to a given vector (for allometric correction)
	rescale_by_landmark_distance	Rescale configurations of landmarks based on inter-landmark distances
	reversePCA	Obtain original variables from PC scores and mean
	rotate_landmarks	Apply a user-defined rotation of a landmark configuration
Phylogenetic Comparative Analysis	Kmultparallel	Parallelised computation of Adams' Kmult (for distributions of trees)
Quality Control and Diagnostics	LM_relativepos_check	Check relative position of landmarks against a reference specimen
Dimensionality Reduction	parallel_analysis	Perform parallel analysis to determine number of principal components to retain

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