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 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.

Copy Link

Version

Install

install.packages('geomorph')

Monthly Downloads

4,399

Version

4.0.6

License

GPL (>= 3)

Issues

Pull Requests

Stars

Forks

Maintainer

Dean Adams

Last Published

August 31st, 2023

Functions in geomorph (4.0.6)

compare.ZVrel

Comparisons of Effect Sizes from Overall Integration Analyses
compare.CR

Comparisons of Effect Sizes from Modularity Analyses
compare.pls

Comparisons of Effect Sizes from Partial Least Squares
buildtemplate

Build 3D surface template
compare.evol.rates

Comparing net rates of shape evolution on phylogenies
arrayspecs

Convert landmark data matrix into array (p x k x n)
combine.subsets

Combine separate landmark configurations
compare.multi.evol.rates

Comparing net rates of evolution among traits on phylogenies
compare.physignal.z

Comparisons of Phylogenetic Signal Effect Sizes
bilat.symmetry

Analysis of bilateral symmetry
coords.subset

Subset landmark coordinates via a factor
define.sliders

Select points to "slide" along curves
define.links

Define links between landmarks
digit.fixed

Digitize 3D landmarks on mesh3d object
digitize2d

Digitize 2D landmarks on .jpg files
estimate.missing

Estimate locations of missing landmarks
digit.curves

Calculate semilandmarks along a curve
define.modules

Define modules (landmark partitions)
editTemplate

Edit 3D template
digitsurface

Digitize 3D fixed landmarks and surface semilandmarks
hummingbirds

Landmark data from hummingbird bills (includes sliding semilandmarks on curves)
geomorph-package

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

Create a data frame with shape data
gm.prcomp

Principal and phylogenetically-aligned components analysis of shape data
globalIntegration

Quantify global integration relative to self-similarity
integration.Vrel

Quantify integration in a set of traits
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
mshape

Estimate mean shape for a set of aligned specimens
mosquito

Landmarks on mosquito wings
lizards

Dorsal head shape data of lizards
na.omit.geomorph.data.frame

Handle missing values in rrpp.data.frame objects
integration.test

Quantify morphological integration between modules
larvalMorph

Head and tail shapes of larval salamanders
morphol.disparity

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

Evaluate the degree of modular signal in shape data
gpagen

Generalized Procrustes analysis of points, curves, and surfaces
interlmkdist

Calculate linear distances between landmarks
make_ggplot

Convert geomorph plots to ggplot objects
gridPar

Set up parameters for grids, points, and links in plotRefToTarget
physignal.z

Assessing phylogenetic signal effect size in Procrustes shape variables
plethShapeFood

Head shape and food use data from Plethodon salamanders
plot.CR

Plot Function for geomorph
physignal

Assessing phylogenetic signal in Procrustes shape variables
phylo.modularity

Evaluate the degree of phylogenetic modular signal in Procrustes shape variables
picknplot.shape

Pick points in geomorph scatterplots to visualize shape variation
phylo.integration

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

Plot Function for geomorph
plot.gm.prcomp

Plot Function for geomorph
plethspecies

Head shape and phylogenetic relationships for several Plethodon salamander species
plot.mshape

Plot Function for geomorph
plot.physignal

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
plethodon

Landmark data from Plethodon salamander heads
plotRefToTarget

Plot shape differences between a reference and target specimen
plot.bilat.symmetry

Plot Function for geomorph
plot.evolrate

Plot Function for geomorph
plot.pls

Plot Function for geomorph
plot.physignal.z

Plot Function for geomorph
plotOutliers

Find potential outliers
print.compare.CR

Print/Summary Function for geomorph
print.evolrate1

Print/Summary Function for geomorph
plotAllometry

Plotting to assist visualization of shape-size covariation (allometry)
print.compare.ZVrel

Print/Summary function for geomorph
print.evolrate

Print/Summary Function for geomorph
print.gpagen

Print/Summary Function for geomorph
print.CR.phylo

Print/Summary Function for geomorph
print.compare.physignal.z

Print/Summary Function for geomorph
plotAllSpecimens

Plot landmark coordinates for all specimens
print.bilat.symmetry

Print/Summary Function for geomorph
print.combined.set

Print/Summary Function for geomorph
plot.procD.lm

Plot Function for geomorph
print.geomorphShapes

Print/Summary function for geomorph
procD.lm

Procrustes ANOVA/regression for Procrustes shape variables
print.morphol.disparity

Print/Summary Function for geomorph
readland.nts

Read landmark data matrix from nts file
print.physignal

Print/Summary Function for geomorph
readland.fcsv

Read landmark data matrix from fcsv file
print.gm.prcomp

Print/Summary function for geomorph
print.physignal.z

Print/Summary Function for geomorph
rotate.coords

Rotate or flip landmark or coordinate configurations
procD.pgls

Phylogenetic ANOVA/regression for Procrustes shape variables
print.pls

Print/Summary Function for geomorph
scallopPLY

3D scan of a scallop shell from a .ply file in mesh3d format
print.compare.pls

Print/Summary Function for geomorph
pupfish

Landmarks on pupfish
readland.shapes

Read landmark data from a shapes object (StereoMorph)
ratland

Landmark data from dataset rat
print.procD.lm

Print/Summary Function for geomorph
shapeHulls

Update Plots with Convex Hulls for Groups
summary.evolrate1

Print/Summary Function for geomorph
summary.CR.phylo

Print/Summary Function for geomorph
summary.geomorphShapes

Print/Summary Function for geomorph
readmulti.tps

Read and combine multiple tps files
readmulti.nts

Read and combine multiple nts files
summary.bilat.symmetry

Print/Summary Function for geomorph
summary.compare.ZVrel

Print/Summary Function for geomorph
summary.physignal

Print/Summary Function for geomorph
summary.compare.pls

Print/Summary Function for geomorph
shape.predictor

Shape prediction from numeric predictors
read.morphologika

Read landmark data from Morphologika file(s)
summary.morphol.disparity

Print/Summary Function for geomorph
readland.tps

Read landmark data from tps file
summary.pls

Print/Summary Function for geomorph
summary.compare.CR

Print/Summary Function for geomorph
scallops

Landmark data from scallop shells
summary.combined.set

Print/Summary Function for geomorph
read.ply

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

Print/Summary Function for geomorph
summary.procD.lm

Print/Summary Function for geomorph
summary.CR

Print/Summary Function for geomorph
two.d.array

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

Print/Summary Function for geomorph
summary.gpagen

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
writeland.tps

Write landmark data to tps file
summary.compare.physignal.z

Print/Summary Function for geomorph
summary.physignal.z

Print/Summary Function for geomorph
two.b.pls

Two-block partial least squares analysis for Procrustes shape variables