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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

3.3.2

License

GPL (>= 2)

Issues

Pull Requests

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Maintainer

Last Published

January 12th, 2021

Functions in geomorph (3.3.2)

compare.CR

Comparisons of Effect Sizes from Modularity Analyses
arrayspecs

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

Define links between landmarks
coords.subset

Subset landmark coordinates via a factor
buildtemplate

Build 3D surface template
compare.evol.rates

Comparing net rates of shape evolution on phylogenies
combine.subsets

Combine separate landmark configurations
compare.multi.evol.rates

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

Analysis of bilateral symmetry
compare.pls

Comparisons of Effect Sizes from Partial Least Squares
digit.curves

Calculate semilandmarks along a curve
digitize2d

Digitize 2D landmarks on .jpg files
digit.fixed

Digitize 3D landmarks on mesh3d object
define.modules

Define modules (landmark partitions)
digitsurface

Digitize 3D fixed landmarks and surface semilandmarks
define.sliders

Select points to "slide" along curves
estimate.missing

Estimate locations of missing landmarks
editTemplate

Edit 3D template
interlmkdist

Calculate linear distances between landmarks
larvalMorph

Head and tail shapes of larval salamanders
gpagen

Generalized Procrustes analysis of points, curves, and surfaces
fixed.angle

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

Identify specimen closest to the mean of a set of Procrustes shape variables
gridPar

Set up parameters for grids, points, and links in plotRefToTarget
globalIntegration

Quantify global integration relative to self-similarity
gm.prcomp

Principal and phylogenetically-aligned components analysis of shape data
hummingbirds

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

Quantify morphological integration between modules
geomorph-package

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

Create a data frame with shape data
phylo.modularity

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

Head shape and food use data from Plethodon salamanders
phylo.integration

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

Assessing phylogenetic signal in Procrustes shape variables
picknplot.shape

Pick points in geomorph scatterplots to visualize shape variation
mshape

Estimate mean shape for a set of aligned specimens
plot.gm.prcomp

Plot Function for geomorph
plot.gpagen

Plot Function for geomorph
print.CR

Print/Summary Function for geomorph
plotspec

Plot 3D specimen, fixed landmarks and surface semilandmarks
plotTangentSpace

Deprecated and defunct functions in geomorph
mosquito

Landmarks on mosquito wings
morphol.disparity

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

Plot Function for geomorph
plot.CR.phylo

Plot Function for geomorph
plotRefToTarget

Plot shape differences between a reference and target specimen
plot.physignal

Plot Function for geomorph
plot.mshape

Plot Function for geomorph
plethodon

Landmark data from Plethodon salamander heads
plotAllSpecimens

Plot landmark coordinates for all specimens
plotAllometry

Plotting to assist visualization of shape-size covariation (allometry)
print.combined.set

Print/Summary Function for geomorph
print.geomorphShapes

Print/Summary function for geomorph
print.evolrate1

Print/Summary Function for geomorph
procD.pgls

Phylogenetic ANOVA/regression for Procrustes shape variables
procD.lm

Procrustes ANOVA/regression for Procrustes shape variables
plotGMPhyloMorphoSpace

Deprecated and defunct functions in geomorph
lizards

Dorsal head shape data of lizards
modularity.test

Evaluate the degree of modular signal in shape data
plot.pls

Plot Function for geomorph
plot.bilat.symmetry

Plot Function for geomorph
plot.evolrate

Plot Function for geomorph
print.CR.phylo

Print/Summary Function for geomorph
summary.combined.set

Print/Summary Function for geomorph
plotOutliers

Find potential outliers
print.bilat.symmetry

Print/Summary Function for geomorph
plot.procD.lm

Plot Function for geomorph
print.evolrate

Print/Summary Function for geomorph
read.morphologika

Read landmark data from Morphologika file(s)
plethspecies

Head shape and phylogenetic relationships for several Plethodon salamander species
read.ply

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

Print/Summary Function for geomorph
shape.predictor

Shape prediction from numeric predictors
scallops

Landmark data from scallop shells
summary.CR.phylo

Print/Summary Function for geomorph
print.pls

Print/Summary Function for geomorph
summary.bilat.symmetry

Print/Summary Function for geomorph
readland.fcsv

Read landmark data matrix from fcsv file
summary.compare.CR

Print/Summary Function for geomorph
print.compare.CR

Print/Summary Function for geomorph
readland.nts

Read landmark data matrix from nts file
shapeHulls

Update Plots with Convex Hulls for Groups
summary.CR

Print/Summary Function for geomorph
print.procD.lm

Print/Summary Function for geomorph
readmulti.tps

Read and combine multiple tps files
readmulti.nts

Read and combine multiple nts files
summary.evolrate1

Print/Summary Function for geomorph
pupfish

Landmarks on pupfish
summary.pls

Print/Summary Function for geomorph
summary.geomorphShapes

Print/Summary Function for geomorph
summary.procD.lm

Print/Summary Function for geomorph
two.b.pls

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

Write landmark data to tps file
summary.gpagen

Print/Summary Function for geomorph
summary.gm.prcomp

Print/Summary Function for geomorph
two.d.array

Convert (p x k x n) data array into 2D data matrix
print.gpagen

Print/Summary Function for geomorph
print.gm.prcomp

Print/Summary function for geomorph
readland.tps

Read landmark data from tps file
print.morphol.disparity

Print/Summary Function for geomorph
ratland

Landmark data from dataset rat
readland.shapes

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

Print/Summary Function for geomorph
scallopPLY

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

Rotate or flip landmark or coordinate configurations
summary.morphol.disparity

Print/Summary Function for geomorph
summary.physignal

Print/Summary Function for geomorph
summary.evolrate

Print/Summary Function for geomorph
summary.compare.pls

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