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geomorph (version 1.1-6)

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

1,803

Version

1.1-6

License

GPL (>= 2)

Maintainer

Dean Adams

Last Published

January 28th, 2014

Functions in geomorph (1.1-6)

fixed.angle

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

Plot allometric patterns in landmark data
ratland

Landmark data from dataset rat
define.sliders.2d

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

Build 3D surface template
curves2d

Defunct functions in geomorph
read.vrml

Read landmark data from vrml files
compare.modular.partitions

Compare modular signal to alternative landmark subsets
arrayspecs

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

Quantify morphological integration between two modules
mshape

Estimate mean shape for a set of aligned specimens
mosquito

landmarks on mosquito wings
trajectory.analysis

Quantify and compare shape change trajectories
read.ply

Read mesh data (vertices and faces) from ply files
define.sliders.3d

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

Plot shape differences between a reference and target specimen
motionpaths

Simulated motion paths
procD.lm

Procrustes ANOVA/regression for shape data
pairwiseD.test

Pairwise Group Comparisons
digitsurface

Digitize 3D fixed landmarks and surface semilandmarks.
readmulti.nts

Read landmark data from multiple nts files
digit.curves

Defunct functions in geomorph
digit.fixed

Digitize 3D landmarks
readland.tps

Read landmark data from tps file
scallopPLY

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

Landmark data from hummingbird bills (includes sliding semilandmarks on curves)
digitize2d

Digitize 2D landmarks.
bilat.symmetry

Analysis of bilateral symmetry
plotAllSpecimens

Plot landmark coordinates for all specimens
plethodon

Landmark data from Plethodon salamander heads
plotspec

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

Plot specimens in tangent space
two.d.array

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

Geometric morphometric analyses for 2D/3D data
gpagen

Generalized Procrustes analysis of points, curves, and surfaces
compare.evol.rates

Comparing rates of shape evolution on phylogenies
physignal

Assessing phylogenetic signal in morphometric data
plethspecies

Average head shape and phylogenetic relationships for several Plethodon salamander species
scallops

Landmark data from scallop shells
writeland.tps

Write landmark data to tps file
readland.nts

Read landmark data matrix from nts file
estimate.missing

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

Edit 3D template
plotGMPhyloMorphoSpace

Plot phylogenetic tree and specimens in tangent space
read.morphologika

Read 3D landmark data from Morphologika files