Learn R Programming

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

geomorph

Geomorph is a software package for performing all stages of geometric morphometric shape analysis of landmark points and curves in 2-and-3-dimensions as well as 3D surfaces in the R statistical computing environment. This repository is dedicated to providing beta versions between CRAN uploads. Details of the installion can be found here: http://geomorphpackage.blogspot.com.au/p/installing-geomorph.html .

To install the current geomorph R-package from CRAN:

Within R:

install.packages("geomorph")

To install the current version of geomorph R-package from Github using devtools:

Within R:

install.packages("devtools")

devtools::install_github("geomorphR/geomorph")

This installs a stable release of the current version of geomorph on CRAN, allowing us to quickly fix errors that slip thorugh the cracks and are uploaded with the CRAN version.

To install the Development version (beta) of geomorph R-package from Github using devtools:

Within R:

install.packages("devtools")

devtools::install_github("geomorphR/geomorph",ref = "Develop")

##NOTE FOR THE PRE-RELEASE (BETA) VERSION: We strongly discourage you from publishing results with this version, unless you check with the authors first.

Copy Link

Version

Install

install.packages('geomorph')

Monthly Downloads

2,592

Version

3.0.2

License

GPL (>= 2)

Maintainer

Dean Adams

Last Published

July 19th, 2016

Functions in geomorph (3.0.2)

arrayspecs

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

Define modules (landmark partitions)
define.links

Define links between landmarks
compare.multi.evol.rates

Comparing rates of shape evolution among traits on phylogenies
compare.evol.rates

Comparing rates of shape evolution on phylogenies
bilat.symmetry

Analysis of bilateral symmetry
compare.modular.partitions

Deprecated functions in geomorph
buildtemplate

Build 3D surface template
define.sliders

Select points to "slide" along curves
advanced.procD.lm

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

Calculate semilandmarks along a curve
digitize2d

Digitize 2D landmarks on .jpg files
digit.fixed

Digitize 3D landmarks on mesh3d object
digitsurface

Digitize 3D fixed landmarks and surface semilandmarks
geomorph-package

Geometric morphometric analyses for 2D/3D data
geomorph.data.frame

Create a data frame with shape data
estimate.missing

Estimate locations of missing landmarks
editTemplate

Edit 3D template
morphol.integr

Deprecated functions in geomorph
mosquito

Landmarks on mosquito wings
globalIntegration

Quantify global integration relative to self-similarity
gridPar

Set up parameters for grids, points, and links in plotRefToTarget
morphol.disparity

Morphological disparity for one or more groups of specimens
modularity.test

Evaluate the degree of modular signal in morphometric datasets
gpagen

Generalized Procrustes analysis of points, curves, and surfaces
hummingbirds

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

Identify specimen closest to the mean of a set of aligned specimens
fixed.angle

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

Tail-shapes of larval salamanders
integration.test

Quantify morphological integration between modules
physignal

Assessing phylogenetic signal in morphometric data
plethodon

Landmark data from Plethodon salamander heads
phylo.modularity

Evaluate the degree of phylogenetic modular signal in morphometric datasets
phylo.pls

Deprecated functions in geomorph
mshape

Estimate mean shape for a set of aligned specimens
motionpaths

Simulated motion paths
plot.procD.allometry

Plot Function for geomorph
plethspecies

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

Head shape and food use data from Plethodon salamanders
plot.procD.lm

Plot Function for geomorph
plot.evolrate

Plot Function for geomorph
plotAllometry

Deprecated functions in geomorph
print.CR

Print/Summary Function for geomorph
plot.trajectory.analysis

Plot Function for geomorph
plot.gpagen

Plot Function for geomorph
print.CR.phylo

Print/Summary Function for geomorph
plot.pls

Plot Function for geomorph
plot.physignal

Plot Function for geomorph
print.advanced.procD.lm

Print/Summary Function for geomorph
print.bilat.symmetry

Print/Summary Function for geomorph
print.gpagen

Print/Summary Function for geomorph
print.morphol.disparity

Print/Summary Function for geomorph
procD.pgls

Phylogenetic ANOVA/regression for shape data
plot.CR

Plot Function for geomorph
pupfish

Landmarks on pupfish
plotspec

Plot 3D specimen, fixed landmarks and surface semilandmarks
plot.CR.phylo

Plot Function for geomorph
print.physignal

Print/Summary Function for geomorph
plotTangentSpace

Plot specimens in tangent space
print.plotTangentSpace

Print/Summary Function for geomorph
print.trajectory.analysis

Print/Summary Function for geomorph
print.procD.lm

Print/Summary Function for geomorph
summary.advanced.procD.lm

Print/Summary Function for geomorph
summary.bilat.symmetry

Print/Summary Function for geomorph
plot.advanced.procD.lm

Plot Function for geomorph
phylo.integration

Quantify phylogenetic morphological integration between two or more sets of variables under Brownian motion
nested.update

Update procD.lm objects with nested effects
plotRefToTarget

Plot shape differences between a reference and target specimen
plotOutliers

Find potential outliers
plot.bilat.symmetry

Plot Function for geomorph
readland.nts

Read landmark data matrix from nts file
print.pls

Print/Summary Function for geomorph
plotAllSpecimens

Plot landmark coordinates for all specimens
read.ply

Read mesh data (vertices and faces) from ply files
print.procD.allometry

Print/Summary Function for geomorph
plotGMPhyloMorphoSpace

Plot phylogenetic tree and specimens in tangent space
procD.lm

Procrustes ANOVA/regression for shape data
procD.allometry

Procrustes ANOVA/regression, specifically for shape-size covariation (allometry)
summary.gpagen

Print/Summary Function for geomorph
summary.morphol.disparity

Print/Summary Function for geomorph
ratland

Landmark data from dataset rat
summary.evolrate

Print/Summary Function for geomorph
read.morphologika

Read landmark data from Morphologika file
summary.pls

Print/Summary Function for geomorph
summary.evolrate1

Print/Summary Function for geomorph
summary.procD.allometry

Print/Summary Function for geomorph
print.evolrate1

Print/Summary Function for geomorph
print.evolrate

Print/Summary Function for geomorph
scallopPLY

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

Landmark data from scallop shells
summary.procD.lm

Print/Summary Function for geomorph
summary.trajectory.analysis

Print/Summary Function for geomorph
summary.physignal

Print/Summary Function for geomorph
readland.tps

Read landmark data from tps file
summary.plotTangentSpace

Print/Summary Function for geomorph
readmulti.nts

Read landmark data from multiple nts files
two.d.array

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

Creates a mesh3d object warped to the mean shape
summary.CR.phylo

Print/Summary Function for geomorph
summary.CR

Print/Summary Function for geomorph
trajectory.analysis

Quantify and compare shape change trajectories
warpRefOutline

Creates a 2D outline warped to the mean shape
two.b.pls

Two-block partial least squares analysis for shape data
writeland.tps

Write landmark data to tps file