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

4.0.5

License

GPL (>= 3)

Issues

Pull Requests

Stars

Forks

Maintainer

Dean Adams

Last Published

January 16th, 2023

Functions in geomorph (4.0.5)

compare.multi.evol.rates

Comparing net rates of evolution among traits on phylogenies
combine.subsets

Combine separate landmark configurations
define.modules

Define modules (landmark partitions)
digit.fixed

Digitize 3D landmarks on mesh3d object
digitsurface

Digitize 3D fixed landmarks and surface semilandmarks
digit.curves

Calculate semilandmarks along a curve
define.links

Define links between landmarks
editTemplate

Edit 3D template
digitize2d

Digitize 2D landmarks on .jpg files
estimate.missing

Estimate locations of missing landmarks
coords.subset

Subset landmark coordinates via a factor
define.sliders

Select points to "slide" along curves
hummingbirds

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

Geometric morphometric analyses for 2D/3D data
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
gpagen

Generalized Procrustes analysis of points, curves, and surfaces
gridPar

Set up parameters for grids, points, and links in plotRefToTarget
geomorph.data.frame

Create a data frame with shape data
globalIntegration

Quantify global integration relative to self-similarity
gm.prcomp

Principal and phylogenetically-aligned components analysis of shape data
integration.Vrel

Quantify integration in a set of traits
mosquito

Landmarks on mosquito wings
interlmkdist

Calculate linear distances between landmarks
make_ggplot

Convert geomorph plots to ggplot objects
mshape

Estimate mean shape for a set of aligned specimens
na.omit.geomorph.data.frame

Handle missing values in rrpp.data.frame objects
morphol.disparity

Morphological disparity for one or more groups of specimens
lizards

Dorsal head shape data of lizards
modularity.test

Evaluate the degree of modular signal in shape data
integration.test

Quantify morphological integration between modules
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
plethodon

Landmark data from Plethodon salamander heads
plot.CR.phylo

Plot Function for geomorph
phylo.modularity

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

Head shape and phylogenetic relationships for several Plethodon salamander species
larvalMorph

Head and tail shapes of larval salamanders
physignal

Assessing phylogenetic signal in Procrustes shape variables
physignal.z

Assessing phylogenetic signal effect size in Procrustes shape variables
plot.CR

Plot Function for geomorph
plot.mshape

Plot Function for geomorph
plot.gpagen

Plot Function for geomorph
plot.pls

Plot Function for geomorph
picknplot.shape

Pick points in geomorph scatterplots to visualize shape variation
plot.physignal

Plot Function for geomorph
plot.procD.lm

Plot Function for geomorph
plot.gm.prcomp

Plot Function for geomorph
plot.physignal.z

Plot Function for geomorph
plotAllSpecimens

Plot landmark coordinates for all specimens
plotRefToTarget

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

Print/Summary Function for geomorph
plotspec

Plot 3D specimen, fixed landmarks and surface semilandmarks
print.combined.set

Print/Summary Function for geomorph
plot.evolrate

Plot Function for geomorph
plot.bilat.symmetry

Plot Function for geomorph
print.compare.ZVrel

Print/Summary function for geomorph
print.morphol.disparity

Print/Summary Function for geomorph
print.compare.CR

Print/Summary Function for geomorph
print.gpagen

Print/Summary Function for geomorph
print.CR

Print/Summary Function for geomorph
plotOutliers

Find potential outliers
print.evolrate1

Print/Summary Function for geomorph
print.physignal

Print/Summary Function for geomorph
print.CR.phylo

Print/Summary Function for geomorph
plotAllometry

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

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

Print/Summary Function for geomorph
print.geomorphShapes

Print/Summary function for geomorph
print.physignal.z

Print/Summary Function for geomorph
print.compare.pls

Print/Summary Function for geomorph
print.gm.prcomp

Print/Summary function for geomorph
readland.fcsv

Read landmark data matrix from fcsv file
print.pls

Print/Summary Function for geomorph
read.morphologika

Read landmark data from Morphologika file(s)
print.procD.lm

Print/Summary Function for geomorph
readland.nts

Read landmark data matrix from nts file
read.ply

Read mesh data (vertices and faces) from ply files
procD.pgls

Phylogenetic ANOVA/regression for Procrustes shape variables
pupfish

Landmarks on pupfish
procD.lm

Procrustes ANOVA/regression for Procrustes shape variables
shape.predictor

Shape prediction from numeric predictors
summary.CR

Print/Summary Function for geomorph
shapeHulls

Update Plots with Convex Hulls for Groups
scallops

Landmark data from scallop shells
ratland

Landmark data from dataset rat
readmulti.nts

Read and combine multiple nts files
readmulti.tps

Read and combine multiple tps files
rotate.coords

Rotate or flip landmark or coordinate configurations
summary.combined.set

Print/Summary Function for geomorph
readland.shapes

Read landmark data from a shapes object (StereoMorph)
summary.CR.phylo

Print/Summary Function for geomorph
summary.evolrate

Print/Summary Function for geomorph
readland.tps

Read landmark data from tps file
summary.compare.ZVrel

Print/Summary Function for geomorph
scallopPLY

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

Print/Summary Function for geomorph
summary.compare.pls

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

Print/Summary Function for geomorph
summary.evolrate1

Print/Summary Function for geomorph
summary.compare.CR

Print/Summary Function for geomorph
summary.physignal.z

Print/Summary Function for geomorph
summary.procD.lm

Print/Summary Function for geomorph
summary.geomorphShapes

Print/Summary Function for geomorph
two.d.array

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

Print/Summary Function for geomorph
summary.gm.prcomp

Print/Summary Function for geomorph
summary.gpagen

Print/Summary Function for geomorph
two.b.pls

Two-block partial least squares analysis for Procrustes shape variables
summary.pls

Print/Summary Function for geomorph
writeland.tps

Write landmark data to tps file
summary.physignal

Print/Summary Function for geomorph
warpRefOutline

Creates a 2D outline warped to the mean shape
warpRefMesh

Creates a mesh3d object warped to the mean shape
arrayspecs

Convert landmark data matrix into array (p x k x n)
compare.pls

Comparisons of Effect Sizes from Partial Least Squares
compare.CR

Comparisons of Effect Sizes from Modularity Analyses
compare.evol.rates

Comparing net rates of shape evolution on phylogenies
buildtemplate

Build 3D surface template
compare.physignal.z

Comparisons of Phylogenetic Signal Effect Sizes
bilat.symmetry

Analysis of bilateral symmetry
compare.ZVrel

Comparisons of Effect Sizes from Overall Integration Analyses