Geometric morphometric analyses of 2d/3d landmark data


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Documentation for package ‘geomorph’ version 2.1.1

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geomorph-package Geometric morphometric analyses for 2D/3D data
arrayspecs Convert landmark data matrix into array (p x k x n)
bilat.symmetry Analysis of bilateral symmetry
buildtemplate Build 3D surface template
compare.evol.rates Comparing rates of shape evolution on phylogenies
compare.modular.partitions Compare modular signal to alternative landmark subsets
define.modules Define modules (landmark partitions)
define.sliders.2d Select points to "slide" along two-dimensional curves.
define.sliders.3d Choose points to "slide" along three-dimensional curves.
digit.fixed Digitize 3D landmarks
digitize2d Digitize 2D landmarks.
digitsurface Digitize 3D fixed landmarks and surface semilandmarks.
editTemplate Edit 3D template
estimate.missing Estimate locations of missing landmarks using the thin-plate spline
findMeanSpec Identify specimen closest to the mean of a set of aligned specimens
fixed.angle Rotate a subset of 2D landmarks to common articulation angle
geomorph Geometric morphometric analyses for 2D/3D data
gpagen Generalized Procrustes analysis of points, curves, and surfaces
hummingbirds Landmark data from hummingbird bills (includes sliding semilandmarks on curves)
morphol.disparity Morphological disparity for one or more groups of specimens
morphol.integr Quantify morphological integration between two modules
mosquito landmarks on mosquito wings
motionpaths Simulated motion paths
mshape Estimate mean shape for a set of aligned specimens
pairwise.slope.test Pairwise Comparisons of Slopes
pairwiseD.test Pairwise Group Comparisons
phylo.pls Quantify phylogenetic morphological integration between two sets of variables
physignal Assessing phylogenetic signal in morphometric data
plethodon Landmark data from Plethodon salamander heads
plethShapeFood Head shape and food use data from Plethodon salamanders
plethspecies Average head shape and phylogenetic relationships for several Plethodon salamander species
plotAllometry Plot allometric patterns in landmark data
plotAllSpecimens Plot landmark coordinates for all specimens
plotGMPhyloMorphoSpace Plot phylogenetic tree and specimens in tangent space
plotRefToTarget Plot shape differences between a reference and target specimen
plotspec Plot 3D specimen, fixed landmarks and surface semilandmarks.
plotTangentSpace Plot specimens in tangent space
procD.lm Procrustes ANOVA/regression for shape data
procD.pgls Phylogenetic ANOVA/regression for shape data
ratland Landmark data from dataset rat
read.morphologika Read landmark data from Morphologika file
read.ply Read mesh data (vertices and faces) from ply files
readland.nts Read landmark data matrix from nts file
readland.tps Read landmark data from tps file
readmulti.nts Read landmark data from multiple nts files
scallopPLY 3D scan of a scallop shell from a .ply file in mesh3d format
scallops Landmark data from scallop shells
trajectory.analysis Quantify and compare shape change trajectories
two.b.pls Two-block partial least squares analysis for shape data
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.
writeland.tps Write landmark data to tps file