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

Files in this package

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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