Geometric morphometric analysis of 2d/3d landmark data


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Documentation for package ‘geomorph’ version 1.1-0

Help Pages

geomorph-package Geometric morphometric analsyes 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.modular.partitions Compare modular signal to alternative landmark subsets
curves2d Select points to "slide" along two-dimensional curves.
digit.curves Select points to "slide" along three-dimensional curves.
digit.fixed Digitize fixed 3D landmarks only.
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
fixed.angle Rotate a subset of 2D landmarks to common articulation angle
geomorph Geometric morphometric analsyes for 2D/3D data
gpagen Generalized Procrustes analyis of points, curves, and surfaces
hummingbirds Landmark data from hummingbird bills (includes sliding semilandmarks on curves)
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
physignal Assessing phylogenetic signal in morphometric data
plethland Landmark data from dataset plethodon
plethodon Landmark data from Plethodon salamander heads
plethspecies Average head shape and phylogenenetic 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
ratland Landmark data from dataset rat
rats Landmark data from rat calvaria
read.morphologika Read 3D landmark data from Morphologika files
read.ply Read landmark data from ply files
read.vrml Read landmark data from .vrml files
readland.nts Read landmark data from nts file
readland.tps Read landmark data from tps file
readmulti.nts Read landmark data from multiple nts files
scallops Landmark data from scallop shells
Specimen4Raw Raw 3D scan data from scallop shell
trajectory.analysis Quantify and compare shape change trajectories
two.d.array Convert (p x k x n) data array into 2D data matrix
writeland.tps Write landmark data to tps file