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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.

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Version

Install

install.packages('geomorph')

Monthly Downloads

2,367

Version

3.0.3

License

GPL (>= 2)

Maintainer

Last Published

September 9th, 2016

Functions in geomorph (3.0.3)

compare.evol.rates

Comparing rates of shape evolution on phylogenies
define.links

Define links between landmarks
buildtemplate

Build 3D surface template
compare.multi.evol.rates

Comparing rates of shape evolution among traits on phylogenies
bilat.symmetry

Analysis of bilateral symmetry
compare.modular.partitions

Deprecated functions in geomorph
arrayspecs

Convert landmark data matrix into array (p x k x n)
advanced.procD.lm

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

Comparisons of Effect Sizes from Partial Least Squares
coords.subset

Subset landmark coordinates via a factor
fixed.angle

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

Identify specimen closest to the mean of a set of aligned specimens
digitize2d

Digitize 2D landmarks on .jpg files
digit.curves

Calculate semilandmarks along a curve
digit.fixed

Digitize 3D landmarks on mesh3d object
editTemplate

Edit 3D template
estimate.missing

Estimate locations of missing landmarks
define.modules

Define modules (landmark partitions)
define.sliders

Select points to "slide" along curves
digitsurface

Digitize 3D fixed landmarks and surface semilandmarks
larvalTails

Tail-shapes of larval salamanders
geomorph-package

Geometric morphometric analyses for 2D/3D data
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
hummingbirds

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

Quantify morphological integration between modules
geomorph.data.frame

Create a data frame with shape data
gpagen

Generalized Procrustes analysis of points, curves, and surfaces
phylo.pls

Deprecated functions in geomorph
mshape

Estimate mean shape for a set of aligned specimens
morphol.integr

Deprecated functions in geomorph
plethodon

Landmark data from Plethodon salamander heads
physignal

Assessing phylogenetic signal in morphometric data
mosquito

Landmarks on mosquito wings
phylo.modularity

Evaluate the degree of phylogenetic modular signal in morphometric datasets
motionpaths

Simulated motion paths
nested.update

Update procD.lm objects with nested effects
phylo.integration

Quantify phylogenetic morphological integration between two or more sets of variables under Brownian motion
plot.CR.phylo

Plot Function for geomorph
plot.CR

Plot Function for geomorph
plot.advanced.procD.lm

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.bilat.symmetry

Plot Function for geomorph
plot.evolrate

Plot Function for geomorph
plot.gpagen

Plot Function for geomorph
plot.physignal

Plot Function for geomorph
plot.pls

Plot Function for geomorph
plotTangentSpace

Plot specimens in tangent space
plotspec

Plot 3D specimen, fixed landmarks and surface semilandmarks
plotAllSpecimens

Plot landmark coordinates for all specimens
plotGMPhyloMorphoSpace

Plot phylogenetic tree and specimens in tangent space
print.bilat.symmetry

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

Print/Summary Function for geomorph
procD.allometry

Procrustes ANOVA/regression, specifically for shape-size covariation (allometry)
print.trajectory.analysis

Print/Summary Function for geomorph
readmulti.nts

Read landmark data from multiple nts files
scallopPLY

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

Print/Summary Function for geomorph
summary.procD.allometry

Print/Summary Function for geomorph
summary.pls

Print/Summary Function for geomorph
plotOutliers

Find potential outliers
summary.procD.lm

Print/Summary Function for geomorph
print.compare.pls

Print/Summary Function for geomorph
plotRefToTarget

Plot shape differences between a reference and target specimen
print.CR

Print/Summary Function for geomorph
pupfish

Landmarks on pupfish
ratland

Landmark data from dataset rat
summary.advanced.procD.lm

Print/Summary Function for geomorph
two.d.array

Convert (p x k x n) data array into 2D data matrix
two.b.pls

Two-block partial least squares analysis for shape data
summary.bilat.symmetry

Print/Summary Function for geomorph
print.evolrate

Print/Summary Function for geomorph
print.CR.phylo

Print/Summary Function for geomorph
procD.pgls

Phylogenetic ANOVA/regression for shape data
procD.lm

Procrustes ANOVA/regression for shape data
read.morphologika

Read landmark data from Morphologika file
read.ply

Read mesh data (vertices and faces) from ply files
summary.CR.phylo

Print/Summary Function for geomorph
summary.evolrate

Print/Summary Function for geomorph
warpRefMesh

Creates a mesh3d object warped to the mean shape
warpRefOutline

Creates a 2D outline warped to the mean shape
plot.procD.lm

Plot Function for geomorph
plot.procD.allometry

Plot Function for geomorph
print.procD.allometry

Print/Summary Function for geomorph
print.procD.lm

Print/Summary Function for geomorph
readland.nts

Read landmark data matrix from nts file
readland.tps

Read landmark data from tps file
summary.compare.pls

Print/Summary Function for geomorph
summary.CR

Print/Summary Function for geomorph
plot.trajectory.analysis

Plot Function for geomorph
plotAllometry

Deprecated functions in geomorph
print.physignal

Print/Summary Function for geomorph
print.morphol.disparity

Print/Summary Function for geomorph
summary.evolrate1

Print/Summary Function for geomorph
summary.gpagen

Print/Summary Function for geomorph
writeland.tps

Write landmark data to tps file
print.evolrate1

Print/Summary Function for geomorph
print.gpagen

Print/Summary Function for geomorph
print.pls

Print/Summary Function for geomorph
print.plotTangentSpace

Print/Summary Function for geomorph
shape.predictor

Shape prediction from numeric predictors
scallops

Landmark data from scallop shells
summary.physignal

Print/Summary Function for geomorph
summary.trajectory.analysis

Print/Summary Function for geomorph
summary.morphol.disparity

Print/Summary Function for geomorph
trajectory.analysis

Quantify and compare shape change trajectories