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geomorph (version 2.0.1)

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

2,592

Version

2.0.1

License

GPL (>= 2)

Maintainer

Dean Adams

Last Published

April 18th, 2014

Functions in geomorph (2.0.1)

digitsurface

Digitize 3D fixed landmarks and surface semilandmarks.
findMeanSpec

Identify specimen closest to the mean of a set of aligned specimens
compare.evol.rates

Comparing rates of shape evolution on phylogenies
fixed.angle

Rotate a subset of 2D landmarks to common articulation angle
buildtemplate

Build 3D surface template
plotRefToTarget

Plot shape differences between a reference and target specimen
arrayspecs

Convert landmark data matrix into array (p x k x n)
define.sliders.3d

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

Plot allometric patterns in landmark data
writeland.tps

Write landmark data to tps file
bilat.symmetry

Analysis of bilateral symmetry
two.d.array

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

Procrustes ANOVA/regression for shape data
define.sliders.2d

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

Simulated motion paths
scallopPLY

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

Plot phylogenetic tree and specimens in tangent space
gpagen

Generalized Procrustes analysis of points, curves, and surfaces
plotspec

Plot 3D specimen, fixed landmarks and surface semilandmarks.
scallops

Landmark data from scallop shells
plethspecies

Average head shape and phylogenetic relationships for several Plethodon salamander species
digit.fixed

Digitize 3D landmarks
physignal

Assessing phylogenetic signal in morphometric data
digitize2d

Digitize 2D landmarks.
read.ply

Read mesh data (vertices and faces) from ply files
read.morphologika

Read landmark data from Morphologika file
readland.tps

Read landmark data from tps file
mosquito

landmarks on mosquito wings
compare.modular.partitions

Compare modular signal to alternative landmark subsets
read.vrml

Defunct functions in geomorph
morphol.integr

Quantify morphological integration between two modules
mshape

Estimate mean shape for a set of aligned specimens
plotTangentSpace

Plot specimens in tangent space
two.b.pls

Two-block partial least squares analysis for shape data
hummingbirds

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

Quantify and compare shape change trajectories
geomorph-package

Geometric morphometric analyses for 2D/3D data
plotAllSpecimens

Plot landmark coordinates for all specimens
estimate.missing

Estimate locations of missing landmarks using the thin-plate spline
plethShapeFood

Head shape and food use data from Plethodon salamanders
warpRefMesh

Creates a mesh3d object warped to the mean shape.
morphol.disparity

Morphological disparity for one or more groups of specimens
phylo.pls

Quantify phylogenetic morphological integration between two sets of variables
pairwiseD.test

Pairwise Group Comparisons
editTemplate

Edit 3D template
readmulti.nts

Read landmark data from multiple nts files
define.modules

Define modules (landmark partitions)
ratland

Landmark data from dataset rat
plethodon

Landmark data from Plethodon salamander heads
readland.nts

Read landmark data matrix from nts file