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.
From Github, using devtools
library(devtools)
install_github("fruciano/GeometricMorphometricsMix", build_vignettes=TRUE)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).
Each function in the package is documented with usage examples and references.
| 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 |