Geometric Morphometric Analyses of 2D/3D Landmark Data


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Documentation for package ‘geomorph’ version 3.1.1

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A B C D E F G H I L M N P R S T W

geomorph-package Geometric morphometric analyses for 2D/3D data

-- A --

advanced.procD.lm Deprecated functions in geomorph
arrayspecs Convert landmark data matrix into array (p x k x n)

-- B --

bilat.symmetry Analysis of bilateral symmetry
buildtemplate Build 3D surface template

-- C --

combine.subsets Combine separate landmark configurations
compare.evol.rates Comparing net rates of shape evolution on phylogenies
compare.multi.evol.rates Comparing net rates of shape evolution among traits on phylogenies
compare.pls Comparisons of Effect Sizes from Partial Least Squares
coords.subset Subset landmark coordinates via a factor

-- D --

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

-- E --

editTemplate Edit 3D template
estimate.missing Estimate locations of missing landmarks

-- F --

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

-- G --

geomorph 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 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

-- H --

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

-- I --

integration.test Quantify morphological integration between modules
interlmkdist Calculate linear distances between landmarks

-- L --

larvalMorph Head and tail shapes of larval salamanders

-- M --

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

-- N --

nested.update Deprecated functions in geomorph

-- P --

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
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
plot.bilat.symmetry Plot Function for geomorph
plot.CR Plot Function for geomorph
plot.CR.phylo 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
plotAllometry Plotting to assist visualization of shape-size covariation (allometry)
plotAllSpecimens Plot landmark coordinates for all specimens
plotGMPhyloMorphoSpace Plot phylogenetic tree and specimens in tangent space
plotOutliers Find potential outliers
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
print.bilat.symmetry Print/Summary Function for geomorph
print.combined.set Print/Summary Function for geomorph
print.compare.pls Print/Summary Function for geomorph
print.CR Print/Summary Function for geomorph
print.CR.phylo 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.plotTangentSpace Print/Summary Function for geomorph
print.pls Print/Summary Function for geomorph
print.procD.lm Print/Summary Function for geomorph
procD.allometry Deprecated functions in geomorph
procD.lm Procrustes ANOVA/regression for Procrustes shape variables
procD.pgls Phylogenetic ANOVA/regression for Procrustes shape variables
pupfish Landmarks on pupfish

-- R --

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.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 landmark data from multiple nts files
rotate.coords Rotate or flip landmark or coordinate configurations

-- S --

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.bilat.symmetry Print/Summary Function for geomorph
summary.combined.set Print/Summary Function for geomorph
summary.compare.pls Print/Summary Function for geomorph
summary.CR Print/Summary Function for geomorph
summary.CR.phylo 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.plotTangentSpace Print/Summary Function for geomorph
summary.pls Print/Summary Function for geomorph
summary.procD.lm Print/Summary Function for geomorph

-- T --

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

-- W --

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