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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

1,761

Version

4.0.8

License

GPL (>= 3)

Issues

Pull Requests

Stars

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Repository

https://github.com/geomorphR/geomorph

Maintainer

Last Published

June 24th, 2024

Functions in geomorph (4.0.8)

Define modules (landmark partitions)

Edit 3D template

Subset landmark coordinates via a factor

Digitize 2D landmarks on .jpg files

Calculate semilandmarks along a curve

Define links between landmarks

estimate.missing

Estimate locations of missing landmarks

Digitize 3D fixed landmarks and surface semilandmarks

Select points to "slide" along curves

Digitize 3D landmarks on mesh3d object

Principal and phylogenetically-aligned components analysis of shape data

geomorph-package

Geometric morphometric analyses for 2D/3D data

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

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

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

Generalized Procrustes analysis of points, curves, and surfaces

geomorph.data.frame

Create a data frame with shape data

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

Estimate mean shape for a set of aligned specimens

modularity.test

Evaluate the degree of modular signal in shape data

Calculate linear distances between landmarks

Dorsal head shape data of lizards

Head and tail shapes of larval salamanders

integration.Vrel

Quantify integration in a set of traits

Convert geomorph plots to ggplot objects

integration.test

Quantify morphological integration between modules

morphol.disparity

Morphological disparity for one or more groups of specimens

Landmarks on mosquito wings

Head shape and food use data from Plethodon salamanders

phylo.modularity

Evaluate the degree of phylogenetic modular signal in Procrustes shape variables

na.omit.geomorph.data.frame

Handle missing values in rrpp.data.frame objects

Assessing phylogenetic signal in Procrustes shape variables

phylo.integration

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

Head shape and phylogenetic relationships for several Plethodon salamander species

Assessing phylogenetic signal effect size in Procrustes shape variables

Plot Function for geomorph

Plot Function for geomorph

Plot Function for geomorph

Landmark data from Plethodon salamander heads

picknplot.shape

Pick points in geomorph scatterplots to visualize shape variation

Plot Function for geomorph

Plot Function for geomorph

Plot Function for geomorph

plot.physignal.z

Plot Function for geomorph

Plot Function for geomorph

Plot Function for geomorph

Print/Summary Function for geomorph

Find potential outliers

print.combined.set

Print/Summary Function for geomorph

plotRefToTarget

Plot shape differences between a reference and target specimen

plot.bilat.symmetry

Plot Function for geomorph

plotAllSpecimens

Plot landmark coordinates for all specimens

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

print.compare.ZVrel

Print/Summary function for geomorph

print.gm.prcomp

Print/Summary function for geomorph

print.compare.physignal.z

Print/Summary Function for geomorph

Print/Summary Function for geomorph

print.evolrate1

Print/Summary Function for geomorph

print.geomorphShapes

Print/Summary function for geomorph

print.compare.CR

Print/Summary Function for geomorph

Plot Function for geomorph

Print/Summary Function for geomorph

Procrustes ANOVA/regression for Procrustes shape variables

print.compare.pls

Print/Summary Function for geomorph

print.physignal

Print/Summary Function for geomorph

print.morphol.disparity

Print/Summary Function for geomorph

Print/Summary Function for geomorph

print.bilat.symmetry

Print/Summary Function for geomorph

Plot 3D specimen, fixed landmarks and surface semilandmarks

read.morphologika

Read landmark data from Morphologika file(s)

Landmark data from dataset rat

print.physignal.z

Print/Summary Function for geomorph

Print/Summary Function for geomorph

Read mesh data (vertices and faces) from ply files

Read landmark data matrix from fcsv file

Print/Summary Function for geomorph

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

readland.shapes

Read landmark data from a shapes object (StereoMorph)

Read landmark data matrix from nts file

shape.predictor

Shape prediction from numeric predictors

Read and combine multiple tps files

Rotate or flip landmark or coordinate configurations

Update Plots with Convex Hulls for Groups

Landmarks on pupfish

Phylogenetic ANOVA/regression for Procrustes shape variables

Print/Summary Function for geomorph

Landmark data from scallop shells

Read landmark data from tps file

summary.CR.phylo

Print/Summary Function for geomorph

summary.compare.pls

Print/Summary Function for geomorph

Print/Summary Function for geomorph

Read and combine multiple nts files

summary.evolrate1

Print/Summary Function for geomorph

summary.morphol.disparity

Print/Summary Function for geomorph

summary.compare.physignal.z

Print/Summary Function for geomorph

summary.physignal

Print/Summary Function for geomorph

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

summary.compare.ZVrel

Print/Summary Function for geomorph

summary.combined.set

Print/Summary Function for geomorph

summary.compare.CR

Print/Summary Function for geomorph

summary.physignal.z

Print/Summary Function for geomorph

Print/Summary Function for geomorph

summary.evolrate

Print/Summary Function for geomorph

Creates a 2D outline warped to the mean shape

Write landmark data to tps file

summary.bilat.symmetry

Print/Summary Function for geomorph

Two-block partial least squares analysis for Procrustes shape variables

summary.geomorphShapes

Print/Summary Function for geomorph

Creates a mesh3d object warped to the mean shape

summary.procD.lm

Print/Summary Function for geomorph

summary.gm.prcomp

Print/Summary Function for geomorph

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

Comparisons of Effect Sizes from Modularity Analyses

compare.physignal.z

Comparisons of Phylogenetic Signal Effect Sizes

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

Build 3D surface template

Analysis of bilateral symmetry

Comparisons of Effect Sizes from Partial Least Squares

Comparisons of Effect Sizes from Overall Integration Analyses