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.

AuthorDean Adams, Michael Collyer, Antigoni Kaliontzopoulou, Emma Sherratt
Date of publication2016-09-09 23:42:37
MaintainerDean Adams <dcadams@iastate.edu>
LicenseGPL (>= 2)
Version3.0.3
http://geomorphr.github.io/geomorph/

View on CRAN

Man pages

advanced.procD.lm: Procrustes ANOVA and pairwise tests for shape data, using...

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: Deprecated functions in geomorph

compare.multi.evol.rates: Comparing rates of shape evolution among traits on...

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 aligned...

fixed.angle: Rotate a subset of 2D landmarks to common articulation angle

geomorph.data.frame: Create a data frame with shape data

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

globalIntegration: Quantify global integration relative to self-similarity

gpagen: Generalized Procrustes analysis of points, curves, and...

gridPar: Set up parameters for grids, points, and links in...

hummingbirds: Landmark data from hummingbird bills (includes sliding...

integration.test: Quantify morphological integration between modules

larvalTails: Tail-shapes of larval salamanders

modularity.test: Evaluate the degree of modular signal in morphometric...

morphol.disparity: Morphological disparity for one or more groups of specimens

morphol.integr: Deprecated functions in geomorph

mosquito: Landmarks on mosquito wings

motionpaths: Simulated motion paths

mshape: Estimate mean shape for a set of aligned specimens

nested.update: Update procD.lm objects with nested effects

phylo.integration: Quantify phylogenetic morphological integration between two...

phylo.modularity: Evaluate the degree of phylogenetic modular signal in...

phylo.pls: Deprecated functions in geomorph

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...

plot.advanced.procD.lm: Plot Function for geomorph

plotAllometry: Deprecated functions in geomorph

plotAllSpecimens: Plot landmark coordinates for all specimens

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

plotGMPhyloMorphoSpace: Plot phylogenetic tree and specimens in tangent space

plot.gpagen: Plot Function for geomorph

plotOutliers: Find potential outliers

plot.physignal: Plot Function for geomorph

plot.pls: Plot Function for geomorph

plot.procD.allometry: Plot Function for geomorph

plot.procD.lm: Plot Function for geomorph

plotRefToTarget: Plot shape differences between a reference and target...

plotspec: Plot 3D specimen, fixed landmarks and surface semilandmarks

plotTangentSpace: Plot specimens in tangent space

plot.trajectory.analysis: Plot Function for geomorph

print.advanced.procD.lm: Print/Summary Function for geomorph

print.bilat.symmetry: 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.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.allometry: Print/Summary Function for geomorph

print.procD.lm: Print/Summary Function for geomorph

print.trajectory.analysis: Print/Summary Function for geomorph

procD.allometry: Procrustes ANOVA/regression, specifically for shape-size...

procD.lm: Procrustes ANOVA/regression for shape data

procD.pgls: Phylogenetic ANOVA/regression for shape data

pupfish: Landmarks on pupfish

ratland: Landmark data from dataset rat

readland.nts: Read landmark data matrix from nts file

readland.tps: Read landmark data from tps file

read.morphologika: Read landmark data from Morphologika file

readmulti.nts: Read landmark data from multiple nts files

read.ply: Read mesh data (vertices and faces) from ply files

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

summary.advanced.procD.lm: Print/Summary Function for geomorph

summary.bilat.symmetry: 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.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.allometry: Print/Summary Function for geomorph

summary.procD.lm: Print/Summary Function for geomorph

summary.trajectory.analysis: Print/Summary Function for geomorph

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

warpRefOutline: Creates a 2D outline warped to the mean shape

writeland.tps: Write landmark data to tps file

Functions

advanced.procD.lm Man page
arrayspecs Man page
bilat.symmetry Man page
buildtemplate Man page
compare.evol.rates Man page
compare.modular.partitions Man page
compare.multi.evol.rates Man page
compare.pls Man page
coords.subset Man page
define.links Man page
define.modules Man page
define.sliders Man page
digit.curves Man page
digit.fixed Man page
digitize2d Man page
digitsurface Man page
editTemplate Man page
estimate.missing Man page
findMeanSpec Man page
fixed.angle Man page
geomorph Man page
geomorph.data.frame Man page
geomorph-package Man page
globalIntegration Man page
gpagen Man page
gridPar Man page
hummingbirds Man page
integration.test Man page
larvalTails Man page
modularity.test Man page
morphol.disparity Man page
morphol.integr Man page
mosquito Man page
motionpaths Man page
mshape Man page
nested.update Man page
phylo.integration Man page
phylo.modularity Man page
phylo.pls Man page
physignal Man page
plethodon Man page
plethShapeFood Man page
plethspecies Man page
plot.advanced.procD.lm Man page
plotAllometry Man page
plotAllSpecimens Man page
plot.bilat.symmetry Man page
plot.CR Man page
plot.CR.phylo Man page
plot.evolrate Man page
plotGMPhyloMorphoSpace Man page
plot.gpagen Man page
plotOutliers Man page
plot.physignal Man page
plot.pls Man page
plot.procD.allometry Man page
plot.procD.lm Man page
plotRefToTarget Man page
plotspec Man page
plotTangentSpace Man page
plot.trajectory.analysis Man page
print.advanced.procD.lm Man page
print.bilat.symmetry Man page
print.compare.pls Man page
print.CR Man page
print.CR.phylo Man page
print.evolrate Man page
print.evolrate1 Man page
print.gpagen Man page
print.morphol.disparity Man page
print.physignal Man page
print.plotTangentSpace Man page
print.pls Man page
print.procD.allometry Man page
print.procD.lm Man page
print.trajectory.analysis Man page
procD.allometry Man page
procD.lm Man page
procD.pgls Man page
pupfish Man page
ratland Man page
readland.nts Man page
readland.tps Man page
read.morphologika Man page
readmulti.nts Man page
read.ply Man page
scallopPLY Man page
scallops Man page
shape.predictor Man page
summary.advanced.procD.lm Man page
summary.bilat.symmetry Man page
summary.compare.pls Man page
summary.CR Man page
summary.CR.phylo Man page
summary.evolrate Man page
summary.evolrate1 Man page
summary.gpagen Man page
summary.morphol.disparity Man page
summary.physignal Man page
summary.plotTangentSpace Man page
summary.pls Man page
summary.procD.allometry Man page
summary.procD.lm Man page
summary.trajectory.analysis Man page
trajectory.analysis Man page
two.b.pls Man page
two.d.array Man page
warpRefMesh Man page
warpRefOutline Man page
writeland.tps Man page

Files

geomorph
geomorph/inst
geomorph/inst/CITATION
geomorph/NAMESPACE
geomorph/NEWS
geomorph/data
geomorph/data/larvalTails.rda
geomorph/data/motionpaths.rda
geomorph/data/ratland.rda
geomorph/data/mosquito.rda
geomorph/data/scallopPLY.rda
geomorph/data/plethodon.rda
geomorph/data/hummingbirds.rda
geomorph/data/pupfish.rda
geomorph/data/plethspecies.rda
geomorph/data/plethShapeFood.rda
geomorph/data/scallops.rda
geomorph/R
geomorph/R/shape.predictor.r
geomorph/R/morphol.disparity.r
geomorph/R/define.links.r
geomorph/R/bilat.symmetry.r
geomorph/R/advanced.procD.lm.r
geomorph/R/procD.lm.r
geomorph/R/findMeanSpec.r
geomorph/R/plotOutliers.r
geomorph/R/readland.tps.r
geomorph/R/geomorph.support.code.r
geomorph/R/plotspec.r
geomorph/R/trajectory.analysis.r
geomorph/R/digit.fixed.r
geomorph/R/procD.pgls.r
geomorph/R/geomorph.data.frame.r
geomorph/R/plotTangentSpace.r
geomorph/R/read.ply.r
geomorph/R/digitsurface.r
geomorph/R/globalIntegration.r
geomorph/R/gridPar.r
geomorph/R/gpagen.r
geomorph/R/geomorph.utils.r
geomorph/R/define.modules.r
geomorph/R/fixed.angle.r
geomorph/R/compare.pls.r
geomorph/R/read.morphologika.r
geomorph/R/estimate.missing.r
geomorph/R/nested.update.r
geomorph/R/integration.test.r
geomorph/R/deprecated.defunct.r
geomorph/R/plotRefToTarget.r
geomorph/R/digitize2d.r
geomorph/R/two.d.array.r
geomorph/R/plotGMPhyloMorphoSpace.r
geomorph/R/phylo.modularity.r
geomorph/R/two.b.pls.r
geomorph/R/build.template.r
geomorph/R/physignal.r
geomorph/R/plotAllSpecimens.r
geomorph/R/digit.curves.r
geomorph/R/readland.nts.r
geomorph/R/modularity.test.r
geomorph/R/procD.allometry.r
geomorph/R/phylo.integration.r
geomorph/R/define.sliders.r
geomorph/R/warpRefMesh.r
geomorph/R/warpRefOutline.r
geomorph/R/writeland.tps.r
geomorph/R/coords.subset.R
geomorph/R/editTemplate.r
geomorph/R/arrayspecs.r
geomorph/R/compare.multi.evol.rates.r
geomorph/R/compare.evol.rates.r
geomorph/R/readmulti.nts.r
geomorph/README.md
geomorph/MD5
geomorph/DESCRIPTION
geomorph/man
geomorph/man/ratland.Rd geomorph/man/plot.advanced.procD.lm.Rd geomorph/man/plethodon.Rd geomorph/man/nested.update.Rd geomorph/man/print.pls.Rd geomorph/man/compare.pls.Rd geomorph/man/plot.trajectory.analysis.Rd geomorph/man/mosquito.Rd geomorph/man/procD.pgls.Rd geomorph/man/plot.procD.allometry.Rd geomorph/man/plethShapeFood.Rd geomorph/man/print.gpagen.Rd geomorph/man/summary.evolrate.Rd geomorph/man/procD.lm.Rd geomorph/man/morphol.integr.Rd geomorph/man/integration.test.Rd geomorph/man/plotAllometry.Rd geomorph/man/print.evolrate.Rd geomorph/man/shape.predictor.Rd geomorph/man/phylo.pls.Rd geomorph/man/plot.CR.Rd geomorph/man/digit.curves.Rd geomorph/man/summary.CR.Rd geomorph/man/print.plotTangentSpace.Rd geomorph/man/plot.evolrate.Rd geomorph/man/digit.fixed.Rd geomorph/man/plotAllSpecimens.Rd geomorph/man/plot.gpagen.Rd geomorph/man/trajectory.analysis.Rd geomorph/man/plot.CR.phylo.Rd geomorph/man/scallopPLY.Rd geomorph/man/summary.physignal.Rd geomorph/man/compare.evol.rates.Rd geomorph/man/read.ply.Rd geomorph/man/print.CR.phylo.Rd geomorph/man/warpRefOutline.Rd geomorph/man/readland.nts.Rd geomorph/man/summary.CR.phylo.Rd geomorph/man/read.morphologika.Rd geomorph/man/digitize2d.Rd geomorph/man/globalIntegration.Rd geomorph/man/summary.procD.lm.Rd geomorph/man/plotGMPhyloMorphoSpace.Rd geomorph/man/physignal.Rd geomorph/man/gridPar.Rd geomorph/man/plethspecies.Rd geomorph/man/plotRefToTarget.Rd geomorph/man/plot.procD.lm.Rd geomorph/man/print.physignal.Rd geomorph/man/mshape.Rd geomorph/man/scallops.Rd geomorph/man/summary.compare.pls.Rd geomorph/man/summary.gpagen.Rd geomorph/man/procD.allometry.Rd geomorph/man/editTemplate.Rd geomorph/man/geomorph-package.Rd geomorph/man/summary.morphol.disparity.Rd geomorph/man/summary.pls.Rd geomorph/man/compare.multi.evol.rates.Rd geomorph/man/findMeanSpec.Rd geomorph/man/compare.modular.partitions.Rd geomorph/man/readmulti.nts.Rd geomorph/man/bilat.symmetry.Rd geomorph/man/summary.procD.allometry.Rd geomorph/man/buildtemplate.Rd geomorph/man/writeland.tps.Rd geomorph/man/plot.physignal.Rd geomorph/man/advanced.procD.lm.Rd geomorph/man/coords.subset.Rd geomorph/man/two.d.array.Rd geomorph/man/print.bilat.symmetry.Rd geomorph/man/warpRefMesh.Rd geomorph/man/estimate.missing.Rd geomorph/man/pupfish.Rd geomorph/man/print.advanced.procD.lm.Rd geomorph/man/digitsurface.Rd geomorph/man/hummingbirds.Rd geomorph/man/print.procD.lm.Rd geomorph/man/summary.bilat.symmetry.Rd geomorph/man/modularity.test.Rd geomorph/man/define.modules.Rd geomorph/man/print.compare.pls.Rd geomorph/man/plot.bilat.symmetry.Rd geomorph/man/arrayspecs.Rd geomorph/man/print.procD.allometry.Rd geomorph/man/plotTangentSpace.Rd geomorph/man/fixed.angle.Rd geomorph/man/summary.evolrate1.Rd geomorph/man/summary.advanced.procD.lm.Rd geomorph/man/plotspec.Rd geomorph/man/phylo.modularity.Rd geomorph/man/phylo.integration.Rd geomorph/man/print.evolrate1.Rd geomorph/man/two.b.pls.Rd geomorph/man/define.links.Rd geomorph/man/print.CR.Rd geomorph/man/morphol.disparity.Rd geomorph/man/print.morphol.disparity.Rd geomorph/man/geomorph.data.frame.Rd geomorph/man/plot.pls.Rd geomorph/man/plotOutliers.Rd geomorph/man/readland.tps.Rd geomorph/man/summary.plotTangentSpace.Rd geomorph/man/print.trajectory.analysis.Rd geomorph/man/gpagen.Rd geomorph/man/larvalTails.Rd geomorph/man/define.sliders.Rd geomorph/man/motionpaths.Rd geomorph/man/summary.trajectory.analysis.Rd

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