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geomorph

Geomorph is a software package for performing all stages of geometric morphometric shape analysis of 2- and 3-dimensional landmark points, as well as semilandmarks on curves and surfaces, in the R statistical computing environment. This repository is dedicated to providing beta versions between CRAN uploads.

To install the current geomorph R-package from CRAN:

Within R:

install.packages("geomorph")

For Mac users: please also install XQuartz from https://www.xquartz.org/. This allows the library(rgl) to function.

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", build_vignettes = TRUE)

This installs a stable release of the current version of geomorph on CRAN, allowing us to quickly fix errors that slip thorough 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", build_vignettes = TRUE)

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

3.1.2

License

GPL (>= 2)

Maintainer

Dean Adams

Last Published

May 20th, 2019

Functions in geomorph (3.1.2)

combine.subsets

Combine separate landmark configurations
bilat.symmetry

Analysis of bilateral symmetry
buildtemplate

Build 3D surface template
interlmkdist

Calculate linear distances between landmarks
larvalMorph

Head and tail shapes of larval salamanders
phylo.modularity

Evaluate the degree of phylogenetic modular signal in Procrustes shape variables
editTemplate

Edit 3D template
physignal

Assessing phylogenetic signal in Procrustes shape variables
estimate.missing

Estimate locations of missing landmarks
geomorph-package

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

Create a data frame with shape data
mosquito

Landmarks on mosquito wings
plot.mshape

Plot Function for geomorph
plot.physignal

Plot Function for geomorph
mshape

Estimate mean shape for a set of aligned specimens
plethodon

Landmark data from Plethodon salamander heads
plotRefToTarget

Plot shape differences between a reference and target specimen
plethspecies

Average head shape and phylogenetic relationships for several Plethodon salamander species
readland.shapes

Read landmark data from a shapes object (StereoMorph)
print.procD.lm

Print/Summary Function for geomorph
print.pls

Print/Summary Function for geomorph
print.CR.phylo

Print/Summary Function for geomorph
print.bilat.symmetry

Print/Summary Function for geomorph
plotTangentSpace

Plot specimens in tangent space
readland.tps

Read landmark data from tps file
compare.multi.evol.rates

Comparing net rates of shape evolution among traits on phylogenies
summary.gpagen

Print/Summary Function for geomorph
summary.gm.prcomp

Print/Summary Function for geomorph
plotspec

Plot 3D specimen, fixed landmarks and surface semilandmarks
summary.morphol.disparity

Print/Summary Function for geomorph
compare.pls

Comparisons of Effect Sizes from Partial Least Squares
summary.physignal

Print/Summary Function for geomorph
print.CR

Print/Summary Function for geomorph
print.geomorphShapes

Print/Summary function for geomorph
digitize2d

Digitize 2D landmarks on .jpg files
procD.allometry

Deprecated functions in geomorph
print.gm.prcomp

Print/Summary function for geomorph
digitsurface

Digitize 3D fixed landmarks and surface semilandmarks
globalIntegration

Quantify global integration relative to self-similarity
gm.prcomp

Principal components analysis of shape data
procD.lm

Procrustes ANOVA/regression for Procrustes shape variables
advanced.procD.lm

Deprecated functions in geomorph
shape.predictor

Shape prediction from numeric predictors
coords.subset

Subset landmark coordinates via a factor
picknplot.shape

Pick points in geomorph scatterplots to visualize shape variation
arrayspecs

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

Update Plots with Convex Hulls for Groups
define.modules

Define modules (landmark partitions)
define.links

Define links between landmarks
plethShapeFood

Head shape and food use data from Plethodon salamanders
plot.gm.prcomp

Plot Function for geomorph
digit.curves

Calculate semilandmarks along a curve
digit.fixed

Digitize 3D landmarks on mesh3d object
summary.evolrate1

Print/Summary Function for geomorph
gpagen

Generalized Procrustes analysis of points, curves, and surfaces
define.sliders

Select points to "slide" along curves
summary.geomorphShapes

Print/Summary Function for geomorph
plot.gpagen

Plot Function for geomorph
hummingbirds

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

Set up parameters for grids, points, and links in plotRefToTarget
integration.test

Quantify morphological integration between modules
warpRefOutline

Creates a 2D outline warped to the mean shape
modularity.test

Evaluate the degree of modular signal in shape data
nested.update

Deprecated functions in geomorph
morphol.disparity

Morphological disparity for one or more groups of specimens
plot.pls

Plot Function for geomorph
writeland.tps

Write landmark data to tps file
plot.CR

Plot Function for geomorph
plot.procD.lm

Plot Function for geomorph
plot.CR.phylo

Plot Function for geomorph
print.gpagen

Print/Summary Function for geomorph
phylo.integration

Quantify phylogenetic morphological integration between two or more sets of variables under Brownian motion
plotGMPhyloMorphoSpace

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

Plot Function for geomorph
print.morphol.disparity

Print/Summary Function for geomorph
plotOutliers

Find potential outliers
print.physignal

Print/Summary Function for geomorph
plot.evolrate

Plot Function for geomorph
print.evolrate

Print/Summary Function for geomorph
print.plotTangentSpace

Print/Summary Function for geomorph
print.evolrate1

Print/Summary Function for geomorph
procD.pgls

Phylogenetic ANOVA/regression for Procrustes shape variables
plotAllSpecimens

Plot landmark coordinates for all specimens
plotAllometry

Plotting to assist visualization of shape-size covariation (allometry)
pupfish

Landmarks on pupfish
print.combined.set

Print/Summary Function for geomorph
read.ply

Read mesh data (vertices and faces) from ply files
print.compare.pls

Print/Summary Function for geomorph
readland.nts

Read landmark data matrix from nts file
scallopPLY

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

Print/Summary Function for geomorph
ratland

Landmark data from dataset rat
read.morphologika

Read landmark data from Morphologika file(s)
scallops

Landmark data from scallop shells
readmulti.nts

Read landmark data from multiple nts files
summary.CR

Print/Summary Function for geomorph
rotate.coords

Rotate or flip landmark or coordinate configurations
summary.CR.phylo

Print/Summary Function for geomorph
summary.combined.set

Print/Summary Function for geomorph
summary.compare.pls

Print/Summary Function for geomorph
summary.plotTangentSpace

Print/Summary Function for geomorph
summary.evolrate

Print/Summary Function for geomorph
two.d.array

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

Print/Summary Function for geomorph
summary.procD.lm

Print/Summary Function for geomorph
warpRefMesh

Creates a mesh3d object warped to the mean shape
two.b.pls

Two-block partial least squares analysis for Procrustes shape variables
compare.evol.rates

Comparing net rates of shape evolution on phylogenies
findMeanSpec

Identify specimen closest to the mean of a set of Procrustes shape variables
fixed.angle

Rotate a subset of 2D landmarks to common articulation angle