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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: https://github.com/geomorphR/geomorph/wiki/Installing-geomorph .

Details on how to get started can be found on the geomorph wiki: https://github.com/geomorphR/geomorph/wiki .

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",ref = "Stable")

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 = "Stable")

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

3.0.4

License

GPL (>= 2)

Maintainer

Last Published

June 8th, 2017

Functions in geomorph (3.0.4)

coords.subset

Subset landmark coordinates via a factor
define.links

Define links between landmarks
bilat.symmetry

Analysis of bilateral symmetry
compare.multi.evol.rates

Comparing net rates of shape evolution among traits on phylogenies
compare.pls

Comparisons of Effect Sizes from Partial Least Squares
compare.evol.rates

Comparing net rates of shape evolution on phylogenies
compare.modular.partitions

Deprecated functions in geomorph
advanced.procD.lm

Procrustes ANOVA and pairwise tests for shape data, using complex linear models
arrayspecs

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

Build 3D surface template
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
gridPar

Set up parameters for grids, points, and links in plotRefToTarget
geomorph-package

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

Create a data frame with shape data
mshape

Estimate mean shape for a set of aligned specimens
nested.update

Update procD.lm objects with nested effects
digitize2d

Digitize 2D landmarks on .jpg files
digitsurface

Digitize 3D fixed landmarks and surface semilandmarks
phylo.integration

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

Evaluate the degree of phylogenetic modular signal in morphometric datasets
digit.curves

Calculate semilandmarks along a curve
digit.fixed

Digitize 3D landmarks on mesh3d object
globalIntegration

Quantify global integration relative to self-similarity
gpagen

Generalized Procrustes analysis of points, curves, and surfaces
hummingbirds

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

Landmarks on mosquito wings
motionpaths

Simulated motion paths
plot.gpagen

Plot Function for geomorph
plot.physignal

Plot Function for geomorph
plotRefToTarget

Plot shape differences between a reference and target specimen
plotTangentSpace

Plot specimens in tangent space
plotspec

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

Deprecated functions in geomorph
physignal

Assessing phylogenetic signal in morphometric data
plot.pls

Plot Function for geomorph
plot.procD.allometry

Plot Function for geomorph
print.evolrate

Print/Summary Function for geomorph
print.evolrate1

Print/Summary Function for geomorph
summary.CR.phylo

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

Print/Summary Function for geomorph
summary.pls

Print/Summary Function for geomorph
summary.procD.allometry

Print/Summary Function for geomorph
larvalTails

Tail-shapes of larval salamanders
modularity.test

Evaluate the degree of modular signal in morphometric datasets
plethShapeFood

Head shape and food use data from Plethodon salamanders
plethodon

Landmark data from Plethodon salamander heads
print.CR

Print/Summary Function for geomorph
procD.allometry

Procrustes ANOVA/regression, specifically for shape-size covariation (allometry)
procD.lm

Procrustes ANOVA/regression for shape data
ratland

Landmark data from dataset rat
plot.procD.lm

Plot Function for geomorph
plot.trajectory.analysis

Plot Function for geomorph
print.CR.phylo

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

Print/Summary Function for geomorph
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
integration.test

Quantify morphological integration between modules
interlmkdist

Calculate linear distances between landmarks
read.morphologika

Read landmark data from Morphologika file(s)
summary.physignal

Print/Summary Function for geomorph
summary.plotTangentSpace

Print/Summary Function for geomorph
morphol.disparity

Morphological disparity for one or more groups of specimens
morphol.integr

Deprecated functions in geomorph
plot.CR.phylo

Plot Function for geomorph
plot.advanced.procD.lm

Plot Function for geomorph
print.physignal

Print/Summary Function for geomorph
print.plotTangentSpace

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.gpagen

Print/Summary Function for geomorph
summary.morphol.disparity

Print/Summary Function for geomorph
summary.procD.lm

Print/Summary Function for geomorph
summary.trajectory.analysis

Print/Summary Function for geomorph
plotAllSpecimens

Plot landmark coordinates for all specimens
plotAllometry

Deprecated functions in geomorph
print.gpagen

Print/Summary Function for geomorph
print.morphol.disparity

Print/Summary Function for geomorph
procD.pgls

Phylogenetic ANOVA/regression for shape data
pupfish

Landmarks on pupfish
read.ply

Read mesh data (vertices and faces) from ply files
readland.nts

Read landmark data matrix from nts file
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
plot.bilat.symmetry

Plot Function for geomorph
plot.evolrate

Plot Function for geomorph
plotGMPhyloMorphoSpace

Plot phylogenetic tree and specimens in tangent space
plotOutliers

Find potential outliers
print.bilat.symmetry

Print/Summary Function for geomorph
print.compare.pls

Print/Summary Function for geomorph
print.pls

Print/Summary Function for geomorph
print.procD.allometry

Print/Summary Function for geomorph
readland.tps

Read landmark data from tps file
summary.bilat.symmetry

Print/Summary Function for geomorph
summary.compare.pls

Print/Summary Function for geomorph
trajectory.analysis

Quantify and compare shape change trajectories
two.b.pls

Two-block partial least squares analysis for shape data
readmulti.nts

Read landmark data from multiple nts files
warpRefOutline

Creates a 2D outline warped to the mean shape
writeland.tps

Write landmark data to tps file
plethspecies

Average head shape and phylogenetic relationships for several Plethodon salamander species
print.procD.lm

Print/Summary Function for geomorph
print.trajectory.analysis

Print/Summary Function for geomorph
shape.predictor

Shape prediction from numeric predictors
summary.CR

Print/Summary Function for geomorph
summary.evolrate

Print/Summary Function for geomorph
summary.evolrate1

Print/Summary Function for geomorph
plot.CR

Plot Function for geomorph