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geomorph

Geometric Morphometric Analyses of 2D/3D Landmark Data

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.

Functions (110)

arrayspecs

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

bilat.symmetry

Analysis of bilateral symmetry

buildtemplate

Build 3D surface template

combine.subsets

Combine separate landmark configurations

compare.CR

Comparisons of Effect Sizes from Modularity Analyses

compare.evol.rates

Comparing net rates of shape evolution on phylogenies

compare.multi.evol.rates

Comparing net rates of evolution among traits on phylogenies

compare.pls

Comparisons of Effect Sizes from Partial Least Squares

coords.subset

Subset landmark coordinates via a factor

define.links

Define links between landmarks

define.modules

Define modules (landmark partitions)

define.sliders

Select points to "slide" along curves

digit.curves

Calculate semilandmarks along a curve

digit.fixed

Digitize 3D landmarks on mesh3d object

digitize2d

Digitize 2D landmarks on .jpg files

digitsurface

Digitize 3D fixed landmarks and surface semilandmarks

editTemplate

Edit 3D template

estimate.missing

Estimate locations of missing landmarks

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

geomorph-package

Geometric morphometric analyses for 2D/3D data

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

gpagen

Generalized Procrustes analysis of points, curves, and surfaces

gridPar

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

hummingbirds

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

integration.test

Quantify morphological integration between modules

interlmkdist

Calculate linear distances between landmarks

larvalMorph

Head and tail shapes of larval salamanders

lizards

Dorsal head shape data of lizards

make_ggplot

Convert geomorph plots to ggplot objects

modularity.test

Evaluate the degree of modular signal in shape data

morphol.disparity

Morphological disparity for one or more groups of specimens

mosquito

Landmarks on mosquito wings

mshape

Estimate mean shape for a set of aligned specimens

phylo.integration

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

phylo.modularity

Evaluate the degree of phylogenetic modular signal in Procrustes shape variables

physignal

Assessing phylogenetic signal in Procrustes shape variables

picknplot.shape

Pick points in geomorph scatterplots to visualize shape variation

plethShapeFood

Head shape and food use data from Plethodon salamanders

plethodon

Landmark data from Plethodon salamander heads

plethspecies

Head shape and phylogenetic relationships for several Plethodon salamander species

plot.CR

Plot Function for geomorph

plot.CR.phylo

Plot Function for geomorph

plot.bilat.symmetry

Plot Function for geomorph

plot.evolrate

Plot Function for geomorph

plot.gm.prcomp

Plot Function for geomorph

plot.gpagen

Plot Function for geomorph

plot.mshape

Plot Function for geomorph

plot.physignal

Plot Function for geomorph

plot.pls

Plot Function for geomorph

plot.procD.lm

Plot Function for geomorph

plotAllSpecimens

Plot landmark coordinates for all specimens

plotAllometry

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

plotOutliers

Find potential outliers

plotRefToTarget

Plot shape differences between a reference and target specimen

plotspec

Plot 3D specimen, fixed landmarks and surface semilandmarks

print.CR

Print/Summary Function for geomorph

print.CR.phylo

Print/Summary Function for geomorph

print.bilat.symmetry

Print/Summary Function for geomorph

print.combined.set

Print/Summary Function for geomorph

print.compare.CR

Print/Summary Function for geomorph

print.compare.pls

Print/Summary Function for geomorph

print.evolrate

Print/Summary Function for geomorph

print.evolrate1

Print/Summary Function for geomorph

print.geomorphShapes

Print/Summary function for geomorph

print.gm.prcomp

Print/Summary function for geomorph

print.gpagen

Print/Summary Function for geomorph

print.morphol.disparity

Print/Summary Function for geomorph

print.physignal

Print/Summary Function for geomorph

print.pls

Print/Summary Function for geomorph

print.procD.lm

Print/Summary Function for geomorph

procD.lm

Procrustes ANOVA/regression for Procrustes shape variables

procD.pgls

Phylogenetic ANOVA/regression for Procrustes shape variables

pupfish

Landmarks on pupfish

ratland

Landmark data from dataset rat

read.morphologika

Read landmark data from Morphologika file(s)

read.ply

Read mesh data (vertices and faces) from ply files

readland.fcsv

Read landmark data matrix from fcsv file

readland.nts

Read landmark data matrix from nts file

readland.shapes

Read landmark data from a shapes object (StereoMorph)

readland.tps

Read landmark data from tps file

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

scallopPLY

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

scallops

Landmark data from scallop shells

shape.predictor

Shape prediction from numeric predictors

shapeHulls

Update Plots with Convex Hulls for Groups

summary.CR

Print/Summary Function for geomorph

summary.CR.phylo

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

summary.compare.pls

Print/Summary Function for geomorph

summary.evolrate

Print/Summary Function for geomorph

summary.evolrate1

Print/Summary Function for geomorph

summary.geomorphShapes

Print/Summary Function for geomorph

summary.gm.prcomp

Print/Summary Function for geomorph

summary.gpagen

Print/Summary Function for geomorph

summary.morphol.disparity

Print/Summary Function for geomorph

summary.physignal

Print/Summary Function for geomorph

summary.pls

Print/Summary Function for geomorph

summary.procD.lm

Print/Summary Function for geomorph

two.b.pls

Two-block partial least squares analysis for Procrustes shape variables

two.d.array

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

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

geomorph

Geometric Morphometric Analyses of 2D/3D Landmark Data

v4.0.0
GPL (>= 2)
Authors
Dean Adams [aut, cre], Michael Collyer [aut], Antigoni Kaliontzopoulou [aut], Erica Baken [aut]
Initial release

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