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.

Author
Dean Adams, Michael Collyer, Antigoni Kaliontzopoulou, Emma Sherratt
Date of publication
2016-09-09 23:42:37
Maintainer
Dean Adams <dcadams@iastate.edu>
License
GPL (>= 2)
Version
3.0.3
URLs

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