Learn R Programming
⚠️There's a newer version (4.0.10) of this package.Take me there.

geomorph (version 1.1-2)

Geometric morphometric analysis 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

Copy Link

Version

Install

install.packages('geomorph')

Monthly Downloads

3,591

Version

1.1-2

License

GPL (>= 2)

Maintainer

Dean Adams

Last Published

July 25th, 2013

Functions in geomorph (1.1-2)

compare.modular.partitions

Compare modular signal to alternative landmark subsets
plotAllSpecimens

Plot landmark coordinates for all specimens
plotRefToTarget

Plot shape differences between a reference and target specimen
curves2d

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

Plot phylogenetic tree and specimens in tangent space
bilat.symmetry

Analysis of bilateral symmetry
digit.fixed

Digitize fixed 3D landmarks only.
morphol.integr

Quantify morphological integration between two modules
arrayspecs

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

Landmark data from Plethodon salamander heads
fixed.angle

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

landmarks on mosquito wings
plotAllometry

Plot allometric patterns in landmark data
pairwiseD.test

Pairwise Group Comarisons
digitize2d

Digitize 2d landmarks.
motionpaths

Simulated motion paths
gpagen

Generalized Procrustes analyis of points, curves, and surfaces
plotTangentSpace

Plot specimens in tangent space
ratland

Landmark data from dataset rat
two.d.array

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

Read landmark data from ply files
hummingbirds

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

Landmark data from scallop shells
readland.nts

Read landmark data from nts file
buildtemplate

Build 3D surface template
rats

Landmark data from rat calvaria
Specimen4Raw

Raw 3D scan data from scallop shell
digit.curves

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

Quantify and compare shape change trajectories
readmulti.nts

Read landmark data from multiple nts files
digitsurface

Digitize 3D fixed landmarks and surface semilandmarks.
readland.tps

Read landmark data from tps file
plethspecies

Average head shape and phylogenenetic relationships for several Plethodon salamander species
read.vrml

Read landmark data from .vrml files
read.morphologika

Read 3D landmark data from Morphologika files
estimate.missing

Estimate locations of missing landmarks using the thin-plate spline
procD.lm

Procrustes ANOVA/regression for shape data
plotspec

Plot 3D specimen, fixed landmarks and surface semilandmarks.
writeland.tps

Write landmark data to tps file
geomorph-package

Geometric morphometric analsyes for 2D/3D data
editTemplate

Edit 3D template
mshape

Estimate mean shape for a set of aligned specimens
physignal

Assessing phylogenetic signal in morphometric data