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geomorph (version 2.1.4)

Geometric Morphometric Analyses of 2d/3D Landmark Data

Description

Read, manipulate, and digitize landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform shape analyses, and provide graphical depictions of shapes and patterns of shape variation.

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Version

Install

install.packages('geomorph')

Monthly Downloads

1,519

Version

2.1.4

License

GPL (>= 2)

Maintainer

Dean Adams

Last Published

April 2nd, 2015

Functions in geomorph (2.1.4)

Define modules (landmark partitions)

morphol.disparity

Morphological disparity for one or more groups of specimens

Build 3D surface template

Analysis of bilateral symmetry

Creates a 2D outline warped to the mean shape.

Landmark data from scallop shells

Identify specimen closest to the mean of a set of aligned specimens

Read landmark data matrix from nts file

Landmark data from dataset rat

Rotate a subset of 2D landmarks to common articulation angle

Pairwise Group Comparisons

Simulated motion paths

Read landmark data from multiple nts files

plotAllSpecimens

Plot landmark coordinates for all specimens

Landmark data from hummingbird bills (includes sliding semilandmarks on curves)

Define links between landmarks

Find potential outliers

Read landmark data from tps file

trajectory.analysis

Quantify and compare shape change trajectories

Write landmark data to tps file

define.sliders.2d

Select points to "slide" along two-dimensional curves.

Head shape and food use data from Plethodon salamanders

Digitize 3D landmarks

Estimate mean shape for a set of aligned specimens

Generalized Procrustes analysis of points, curves, and surfaces

Assessing phylogenetic signal in morphometric data

Digitize 2D landmarks.

3D scan of a scallop shell from a .ply file in mesh3d format

Plot 3D specimen, fixed landmarks and surface semilandmarks.

pairwise.slope.test

Pairwise Comparisons of Slopes

plotGMPhyloMorphoSpace

Plot phylogenetic tree and specimens in tangent space

Creates a mesh3d object warped to the mean shape.

Edit 3D template

Two-block partial least squares analysis for shape data

Convert landmark data matrix into array (p x k x n)

plotTangentSpace

Plot specimens in tangent space

landmarks on mosquito wings

compare.evol.rates

Comparing rates of shape evolution on phylogenies

Quantify morphological integration between two modules

compare.modular.partitions

Compare modular signal to alternative landmark subsets

Plot allometric patterns in landmark data

advanced.procD.lm

Procrustes ANOVA and pairwise tests for shape data, using complex linear models

define.sliders.3d

Select points to "slide" along three-dimensional curves.

read.morphologika

Read landmark data from Morphologika file

Average head shape and phylogenetic relationships for several Plethodon salamander species

geomorph-package

Geometric morphometric analyses for 2D/3D data

Digitize 3D fixed landmarks and surface semilandmarks.

Landmark data from Plethodon salamander heads

Procrustes ANOVA/regression for shape data

Phylogenetic ANOVA/regression for shape data

Quantify phylogenetic morphological integration between two sets of variables

Convert (p x k x n) data array into 2D data matrix

estimate.missing

Estimate locations of missing landmarks

Read mesh data (vertices and faces) from ply files

plotRefToTarget

Plot shape differences between a reference and target specimen

landmarks on pupfish