R: Geometric Morphometric Analyses of 2D and 3D Landmark Data

# Geometric Morphometric Analyses of 2D and 3D Landmark Data

## Documentation for package ‘geomorph’ version 4.1.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

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 --

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

## -- B --

bilat.symmetry | Analysis of bilateral symmetry
build.template | Deprecated functions in geomorph

## -- C --

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.physignal.z | Comparisons of Phylogenetic Signal Effect Sizes
compare.pls | Comparisons of Effect Sizes from Partial Least Squares
compare.ZVrel | Comparisons of Effect Sizes from Overall Integration Analyses
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 | This function has been deprecated, as RGL no longer
digitize2d | Digitize 2D landmarks on .jpg files
digitsurface | This function has been deprecated.

## -- E --

editTemplate | This function has been deprecated.
estimate.missing | Estimate locations of missing landmarks
extended.pgls | Extended Phylogenetic ANOVA/regression for Procrustes shape variables

## -- 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.measurement.error | This function is a wrapper for the function measurement.error in RRPP
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

## -- H --

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

## -- I --

integration.test | Quantify morphological integration between modules
integration.Vrel | Quantify integration in a set of traits
interlmkdist | Calculate linear distances between landmarks

## -- L --

larvalMorph | Head and tail shapes of larval salamanders
lizards | Dorsal head shape data of lizards

## -- M --

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

## -- N --

na.omit.geomorph.data.frame | Handle missing values in rrpp.data.frame objects

## -- 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
physignal.eigen | Assessing dimensions of phylogenetic signal in Procrustes shape variables
physignal.z | Assessing phylogenetic signal effect size 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 | 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.physignal.eigen | Plot Function for geomorph
plot.physignal.z | 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
plotOutliers | Find potential outliers
plotRefToTarget | Plot shape differences between a reference and target specimen
plotspec | Plot 3D specimen, fixed landmarks and surface semilandmarks
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.physignal.z | Print/Summary Function for geomorph
print.compare.pls | Print/Summary Function for geomorph
print.compare.ZVrel | 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.physignal.eigen | Print/Summary Function for geomorph
print.physignal.z | 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
pupfish.ws | 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.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

## -- 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.CR | Print/Summary Function for geomorph
summary.compare.physignal.z | Print/Summary Function for geomorph
summary.compare.pls | Print/Summary Function for geomorph
summary.compare.ZVrel | 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.physignal.eigen | Print/Summary Function for geomorph
summary.physignal.z | 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