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geomorph (version 2.1.2)

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

2,582

Version

2.1.2

License

GPL (>= 2)

Maintainer

Dean Adams

Last Published

November 4th, 2014

Functions in geomorph (2.1.2)

plotRefToTarget

Plot shape differences between a reference and target specimen

estimate.missing

Estimate locations of missing landmarks using the thin-plate spline

Average head shape and phylogenetic relationships for several Plethodon salamander species

pairwise.slope.test

Pairwise Comparisons of Slopes

compare.evol.rates

Comparing rates of shape evolution on phylogenies

Build 3D surface template

Generalized Procrustes analysis of points, curves, and surfaces

Digitize 3D landmarks

Plot allometric patterns in landmark data

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

Define modules (landmark partitions)

read.morphologika

Read landmark data from Morphologika file

compare.modular.partitions

Compare modular signal to alternative landmark subsets

Pairwise Group Comparisons

Digitize 2D landmarks.

trajectory.analysis

Quantify and compare shape change trajectories

morphol.disparity

Morphological disparity for one or more groups of specimens

Quantify phylogenetic morphological integration between two sets of variables

define.sliders.3d

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

Two-block partial least squares analysis for shape data

Digitize 3D fixed landmarks and surface semilandmarks.

Analysis of bilateral symmetry

Edit 3D template

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

define.sliders.2d

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

plotAllSpecimens

Plot landmark coordinates for all specimens

Estimate mean shape for a set of aligned specimens

advanced.procD.lm

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

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

Rotate a subset of 2D landmarks to common articulation angle

Procrustes ANOVA/regression for shape data

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

Head shape and food use data from Plethodon salamanders

Creates a mesh3d object warped to the mean shape.

landmarks on mosquito wings

Quantify morphological integration between two modules

Landmark data from dataset rat

Plot 3D specimen, fixed landmarks and surface semilandmarks.

Phylogenetic ANOVA/regression for shape data

Read mesh data (vertices and faces) from ply files

Read landmark data from tps file

Landmark data from Plethodon salamander heads

Read landmark data from multiple nts files

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

Creates a 2D outline warped to the mean shape.

plotGMPhyloMorphoSpace

Plot phylogenetic tree and specimens in tangent space

Write landmark data to tps file

Read landmark data matrix from nts file

plotTangentSpace

Plot specimens in tangent space

Simulated motion paths

geomorph-package

Geometric morphometric analyses for 2D/3D data

Assessing phylogenetic signal in morphometric data

Landmark data from Cyprinodon pecosensis

Landmark data from scallop shells