Package: GeometricMorphometricsMix 0.6.1.1

GeometricMorphometricsMix: Heterogeneous Methods for Shape and Other Multidimensional Data

Tools for geometric morphometric analyses and multidimensional data. Implements methods for morphological disparity analysis using bootstrap and rarefaction, as reviewed in Foote (1997) <doi:10.1146/annurev.ecolsys.28.1.129>. Includes integration and modularity testing, following Fruciano et al. (2013) <doi:10.1371/journal.pone.0069376>, using Escoufier's RV coefficient as test statistic as well as two-block partial least squares - PLS, Rohlf and Corti (2000) <doi:10.1080/106351500750049806>. Also includes vector angle comparisons, orthogonal projection for data correction (Burnaby (1966) <doi:10.2307/2528217>; Fruciano (2016) <doi:10.1007/s00427-016-0537-4>), and parallel analysis for dimensionality reduction (Buja and Eyuboglu (1992) <doi:10.1207/s15327906mbr2704_2>).

Authors:Carmelo Fruciano [aut, cre]

GeometricMorphometricsMix_0.6.1.1.tar.gz
GeometricMorphometricsMix_0.6.1.1.zip(r-4.7-any)GeometricMorphometricsMix_0.6.1.1.zip(r-4.6-any)GeometricMorphometricsMix_0.6.1.1.zip(r-4.5-any)
GeometricMorphometricsMix_0.6.1.1.tgz(r-4.6-any)GeometricMorphometricsMix_0.6.1.1.tgz(r-4.5-any)
GeometricMorphometricsMix_0.6.1.1.tar.gz(r-4.7-any)GeometricMorphometricsMix_0.6.1.1.tar.gz(r-4.6-any)
GeometricMorphometricsMix_0.6.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GeometricMorphometricsMix/json (API)

# Install 'GeometricMorphometricsMix' in R:
install.packages('GeometricMorphometricsMix', repos = c('https://fruciano.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fruciano/geometricmorphometricsmix/issues

Datasets:

On CRAN:

Conda:

5.56 score 4 stars 5 scripts 372 downloads 21 exports 2 dependencies

Last updated from:1c67967c52. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK174
source / vignettesOK242
linux-release-x86_64OK166
macos-release-arm64OK167
macos-oldrel-arm64OK169
windows-develOK130
windows-releaseOK129
windows-oldrelOK181
wasm-releaseOK121

Exports:adjRand_testBTailTestcritical_angledisparity_resampledisparity_testdist_mean_bootEscoufierRVKmultparallelLM_relativepos_checkparallel_analysisplspls_major_axisProjectOrthogonalrepeated_measures_testrescale_by_landmark_distancereversePCArotate_landmarksRVcomparisonRVrarefiedscaled_variance_of_eigenvaluesTestOfAngle

Dependencies:corpcormclust

Analysis of Disparity: Estimating and Comparing How Variable Phenotype Is
Introduction | Basic Concepts | Statistical approaches | Simulate Example Data | Bootstrap Analysis | Rarefaction Analysis | Visualization | Permutation Tests Between Two Groups | Univariate Data Analysis | Advanced: Single Group Analysis | Practical Considerations | Sample Size Effects | Statistic Selection | Interpretation Guidelines | Summary
Rendered fromdisparity_analysis.Rmdusingknitr::rmarkdown

Last update: 2025-09-03
Started: 2025-08-24

Partial Least Squares (PLS) Analysis
Introduction | Simulate Data | Run PLS Analysis | Interpretation | Simulating Data with Expected Significant Covariation | Run PLS Analysis on Associated Data | Interpretation of Associated Data | Using pls_major_axis for Major Axis Projection and Predictions | Major Axis Projection for Original Data | Providing New Data for Prediction | Notes
Rendered frompls_analysis_use_case.Rmdusingknitr::rmarkdown

Last update: 2025-08-23
Started: 2025-08-23

Readme and manuals

Help Manual

Help pageTopics
Test the significance of the adjusted Rand indexadjRand_test
Body arching vector from brown trout studyarching_vector
Brown trout landmark databrown_trout
BTailTest for difference in disparity/morphospace occupationBTailTest
Compute the critical angle for the test of the angle between two multivariate vectorscritical_angle
Resampling-based estimates (bootstrap or rarefaction) of disparity / morphospace occupationdisparity_resample
Permutation test of difference in disparity/morphospace occupationdisparity_test
Bootstrapped distance between two arraysdist_mean_boot
Escoufier RV coefficientEscoufierRV
Check the relative positions for a set of landmarks, compared to a reference specimenLM_relativepos_check
Perform parallel analysisparallel_analysis
Plot method for disparity_resample objectsplot.disparity_resample
Plot method for EscoufierRVrarefy objectsplot.EscoufierRVrarefy
Partial least squares (PLS) analysispls
Major axis predictions for partial least squares (PLS) analysispls_major_axis
Print method for disparity_resample objectsprint.disparity_resample
Print method for EscoufierRVrarefy objectsprint.EscoufierRVrarefy
Project to subspace orthogonal to a vectorProjectOrthogonal
Perform test on two repeated measuresrepeated_measures_test
Rescale landmark data based on interlandmark distancesrescale_by_landmark_distance
'Reverse' PCAreversePCA
User-defined rotation of a landmark configurationrotate_landmarks
Compare Escoufier RV coefficient between groupsRVcomparison
Rarefied version of Escoufier RV coefficientRVrarefied
Compute scaled variance of eigenvaluesscaled_variance_of_eigenvalues
Perform a test of the angle between two multivariate vectorsTestOfAngle