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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.

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Version

Install

install.packages('geomorph')

Monthly Downloads

2,095

Version

4.0.10

License

GPL (>= 3)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/geomorphR/geomorph

Maintainer

Dean Adams

Last Published

February 5th, 2025

Functions in geomorph (4.0.10)

combine.subsets

Combine separate landmark configurations

Comparisons of Effect Sizes from Overall Integration Analyses

Calculate semilandmarks along a curve

estimate.missing

Estimate locations of missing landmarks

Edit 3D template

Digitize 3D fixed landmarks and surface semilandmarks

Digitize 2D landmarks on .jpg files

Define modules (landmark partitions)

Select points to "slide" along curves

Digitize 3D landmarks on mesh3d object

Subset landmark coordinates via a factor

Define links between landmarks

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

geomorph-package

Geometric morphometric analyses for 2D/3D data

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

geomorph.data.frame

Create a data frame with shape data

Generalized Procrustes analysis of points, curves, and surfaces

Extended Phylogenetic ANOVA/regression for Procrustes shape variables

Rotate a subset of 2D landmarks to common articulation angle

globalIntegration

Quantify global integration relative to self-similarity

gm.measurement.error

This function is a wrapper for the function measurement.error in RRPP

Principal and phylogenetically-aligned components analysis of shape data

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

morphol.disparity

Morphological disparity for one or more groups of specimens

Dorsal head shape data of lizards

Head and tail shapes of larval salamanders

Calculate linear distances between landmarks

integration.test

Quantify morphological integration between modules

Convert geomorph plots to ggplot objects

modularity.test

Evaluate the degree of modular signal in shape data

integration.Vrel

Quantify integration in a set of traits

Landmarks on mosquito wings

Estimate mean shape for a set of aligned specimens

Head shape and food use data from Plethodon salamanders

Landmark data from Plethodon salamander heads

na.omit.geomorph.data.frame

Handle missing values in rrpp.data.frame objects

Assessing phylogenetic signal effect size in Procrustes shape variables

Assessing phylogenetic signal in Procrustes shape variables

phylo.integration

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

physignal.eigen

Assessing dimensions of 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

Plot Function for geomorph

Plot Function for geomorph

Plot Function for geomorph

Plot Function for geomorph

plot.bilat.symmetry

Plot Function for geomorph

plot.physignal.eigen

Plot Function for geomorph

Plot Function for geomorph

Plot Function for geomorph

Plot Function for geomorph

Print/Summary Function for geomorph

Print/Summary Function for geomorph

plot.physignal.z

Plot Function for geomorph

print.geomorphShapes

Print/Summary function for geomorph

plotAllSpecimens

Plot landmark coordinates for all specimens

print.compare.pls

Print/Summary Function for geomorph

print.gm.prcomp

Print/Summary function for geomorph

print.compare.physignal.z

Print/Summary Function for geomorph

plotRefToTarget

Plot shape differences between a reference and target specimen

Plot Function for geomorph

Head shape and phylogenetic relationships for several Plethodon salamander species

Print/Summary Function for geomorph

print.evolrate1

Print/Summary Function for geomorph

Print/Summary Function for geomorph

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

Procrustes ANOVA/regression for Procrustes shape variables

Plot 3D specimen, fixed landmarks and surface semilandmarks

print.physignal.z

Print/Summary Function for geomorph

print.compare.ZVrel

Print/Summary function for geomorph

print.compare.CR

Print/Summary Function for geomorph

print.physignal

Print/Summary Function for geomorph

Plot Function for geomorph

print.physignal.eigen

Print/Summary Function for geomorph

Print/Summary Function for geomorph

Read landmark data matrix from fcsv file

Read landmark data matrix from nts file

readland.shapes

Read landmark data from a shapes object (StereoMorph)

read.morphologika

Read landmark data from Morphologika file(s)

Read landmark data from tps file

Find potential outliers

Read mesh data (vertices and faces) from ply files

Phylogenetic ANOVA/regression for Procrustes shape variables

print.bilat.symmetry

Print/Summary Function for geomorph

Print/Summary Function for geomorph

summary.CR.phylo

Print/Summary Function for geomorph

print.combined.set

Print/Summary Function for geomorph

summary.bilat.symmetry

Print/Summary Function for geomorph

summary.combined.set

Print/Summary Function for geomorph

summary.compare.CR

Print/Summary Function for geomorph

print.morphol.disparity

Print/Summary Function for geomorph

Landmark data from scallop shells

summary.compare.ZVrel

Print/Summary Function for geomorph

summary.compare.physignal.z

Print/Summary Function for geomorph

shape.predictor

Shape prediction from numeric predictors

Landmarks on pupfish

summary.morphol.disparity

Print/Summary Function for geomorph

summary.physignal

Print/Summary Function for geomorph

Creates a 2D outline warped to the mean shape

Landmarks on pupfish

Creates a mesh3d object warped to the mean shape

Read and combine multiple nts files

summary.compare.pls

Print/Summary Function for geomorph

Print/Summary Function for geomorph

summary.procD.lm

Print/Summary Function for geomorph

Landmark data from dataset rat

Read and combine multiple tps files

Update Plots with Convex Hulls for Groups

summary.evolrate

Print/Summary Function for geomorph

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

Rotate or flip landmark or coordinate configurations

Two-block partial least squares analysis for Procrustes shape variables

Print/Summary Function for geomorph

summary.geomorphShapes

Print/Summary Function for geomorph

summary.evolrate1

Print/Summary Function for geomorph

Write landmark data to tps file

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

summary.gm.prcomp

Print/Summary Function for geomorph

Print/Summary Function for geomorph

summary.physignal.eigen

Print/Summary Function for geomorph

summary.physignal.z

Print/Summary Function for geomorph

compare.multi.evol.rates

Comparing net rates of evolution among traits on phylogenies

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

Analysis of bilateral symmetry

Comparisons of Effect Sizes from Partial Least Squares

Build 3D surface template

Comparisons of Effect Sizes from Modularity Analyses

compare.evol.rates

Comparing net rates of shape evolution on phylogenies

compare.physignal.z

Comparisons of Phylogenetic Signal Effect Sizes