Learn R Programming

⚠️There's a newer version (4.0.10) of this package.Take me there.

geomorph (version 2.1.6)

Geometric Morphometric Analyses of 2D/3D Landmark Data

Description

Read, manipulate, and digitize landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform shape analyses, and provide graphical depictions of shapes and patterns of shape variation.

Copy Link

Version

Install

install.packages('geomorph')

Monthly Downloads

2,592

Version

2.1.6

License

GPL (>= 2)

Maintainer

Dean Adams

Last Published

June 23rd, 2015

Functions in geomorph (2.1.6)

compare.evol.rates

Comparing rates of shape evolution on phylogenies

Digitize 3D fixed landmarks and surface semilandmarks.

Define links between landmarks

landmarks on mosquito wings

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

estimate.missing

Estimate locations of missing landmarks

pairwise.slope.test

Defunct functions in geomorph

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

Read landmark data from tps file

geomorph-package

Geometric morphometric analyses for 2D/3D data

Calculate semilandmarks along a curve

morphol.disparity

Morphological disparity for one or more groups of specimens

Analysis of bilateral symmetry

define.sliders.2d

Defunct functions in geomorph

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

globalIntegration

Quantify global integration relative to self-similarity

Plot allometric patterns in landmark data

Generalized Procrustes analysis of points, curves, and surfaces

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

advanced.procD.lm

Procrustes ANOVA and pairwise tests for shape data, using complex linear models

Rotate a subset of 2D landmarks to common articulation angle

plotRefToTarget

Plot shape differences between a reference and target specimen

Creates a mesh3d object warped to the mean shape.

Landmark data from Plethodon salamander heads

Identify specimen closest to the mean of a set of aligned specimens

Plot 3D specimen, fixed landmarks and surface semilandmarks.

plotTangentSpace

Plot specimens in tangent space

trajectory.analysis

Quantify and compare shape change trajectories

Digitize 3D landmarks

Procrustes ANOVA/regression for shape data

Defunct functions in geomorph

Define modules (landmark partitions)

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

read.morphologika

Read landmark data from Morphologika file

Read landmark data from multiple nts files

Read mesh data (vertices and faces) from ply files

Find potential outliers

Read landmark data matrix from nts file

landmarks on pupfish

plotAllSpecimens

Plot landmark coordinates for all specimens

Average head shape and phylogenetic relationships for several Plethodon salamander species

Digitize 2D landmarks.

Landmark data from dataset rat

Quantify phylogenetic morphological integration between two sets of variables

Landmark data from scallop shells

Build 3D surface template

Head shape and food use data from Plethodon salamanders

Two-block partial least squares analysis for shape data

Estimate mean shape for a set of aligned specimens

Edit 3D template

Quantify morphological integration between two modules

plotGMPhyloMorphoSpace

Plot phylogenetic tree and specimens in tangent space

Creates a 2D outline warped to the mean shape.

Write landmark data to tps file

compare.modular.partitions

Compare modular signal to alternative landmark subsets

Phylogenetic ANOVA/regression for shape data

Assessing phylogenetic signal in morphometric data

define.sliders.3d

Defunct functions in geomorph

Select points to "slide" along curves.

Simulated motion paths