Calculations and Visualisations Related to Geometric Morphometrics

Documentation for package ‘Morpho’ version 2.12

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A B C D E F G H I K L M N O P Q R S T U V W

A toolbox providing methods for data-acquisition, visualisation and statistical methods related to Geometric Morphometrics and shape analysis

-- A --

align2procSym	align new data to an existing Procrustes registration
angle.calc	calculate angle between two vectors
angleTest	Test whether the direction of two vectors is similar
anonymize	Replace ID-strings of data and associated files.
applyTransform	apply affine transformation to data
applyTransform.default	apply affine transformation to data
applyTransform.matrix	apply affine transformation to data
applyTransform.mesh3d	apply affine transformation to data
areaSphere	compute the area of an n-dimensional hypersphere
areaSpherePart	compute the area of an n-dimensional hypersphere cap
armaGinv	calculate Pseudo-inverse of a Matrix using RcppArmadillo
array2list	reverts list2array, converting an array to a list of matrices
arrMean3	calculate mean of an array
asymPermute	Assess differences in amount and direction of asymmetric variation (only object symmetry)

-- B --

barycenter	calculates the barycenters for all faces of a triangular mesh
bindArr	concatenate multiple arrays/matrices
bone1	predefined colors for bone and skin
bone2	predefined colors for bone and skin
bone3	predefined colors for bone and skin
boneData	Landmarks and a triangular mesh
boneLM	Landmarks and a triangular mesh

-- C --

CAC	calculate common allometric component
cExtract	extract information about fixed landmarks, curves and patches from and atlas generated by "landmark"
checkLM	Visually browse through a sample rendering its landmarks and corresponding surfaces.
checkNA	check for NA values in a matrix (of landmarks)
classify	classify specimen based on between-group PCA or CVA or typprobClass
classify.bgPCA	classify specimen based on between-group PCA or CVA or typprobClass
classify.CVA	classify specimen based on between-group PCA or CVA or typprobClass
classify.typprob	classify specimen based on between-group PCA or CVA or typprobClass
closemeshKD	Project coordinates onto a target triangular surface mesh.
colors	predefined colors for bone and skin
computeArea	Compute area enclosed within an irregular polygon
computeTransform	calculate an affine transformation matrix
covDist	calculates distances and PC-coordinates of covariance matrices
covPCA	calculates distances and PC-coordinates of covariance matrices
covW	calculate the pooled within groups covariance matrix
createAtlas	Create an atlas needed in placePatch
CreateL	Create Matrices necessary for Thin-Plate Spline
createMissingList	create a list with empty entries to be used as missingList in slider3d
crossProduct	calculate the orthogonal complement of a 3D-vector
cSize	calculate Centroid Size for a landmark configuration
cutMeshPlane	cut a mesh by a hyperplane and remove parts above/below that plane
cutSpace	separate a 3D-pointcloud by a hyperplane
CVA	Canonical Variate Analysis

-- D --

data2platonic	creates 3D shapes from data to be saved as triangular meshes
deformGrid2d	visualise differences between two superimposed sets of 2D landmarks
deformGrid3d	visualise differences between two superimposed sets of 3D landmarks

-- E --

equidistantCurve	make a curve equidistant (optionally up/downsampling)
export	plot or save the results of meshDist
export.meshDist	plot or save the results of meshDist
exVar	calculate variance of a distribution stemming from prediction models
exVar.lm	calculate variance of a distribution stemming from prediction models
exVar.mvr	calculate variance of a distribution stemming from prediction models

-- F --

facenormals	Compute face or vertex normals of a triangular mesh
fastKmeans	fast kmeans clustering for 2D or 3D point clouds
file2mesh	Import 3D surface mesh files
find.outliers	Graphical interface to find outliers and/or to switch mislabeld landmarks
fixLMmirror	estimate missing landmarks from their bilateral counterparts
fixLMmirror.array	estimate missing landmarks from their bilateral counterparts
fixLMmirror.matrix	estimate missing landmarks from their bilateral counterparts
fixLMtps	estimate missing landmarks

-- G --

getFaces	find indices of faces that contain specified vertices
getMeaningfulPCs	get number of meaningful Principal components
getOuterViewpoints	Get viewpoints on a sphere around a 3D mesh
getPCscores	Obtain PC-scores for new landmark data
getPCtol	determine the minimum ratio for two subsequent eigenvalues to be considered different
getPLSCommonShape	Get the linear combinations associated with the common shape change in each latent dimension of a pls2B
getPLSfromScores	compute changes associated with 2-Block PLS-scores
getPLSscores	compute 2-Block PLS scores for new data
getPointAlongOutline	Get a point along a line with a given distance from the start of the line
getSides	try to identify bilateral landmarks and sort them by side
getTrafo4x4	get 4x4 Transformation matrix
getTrafo4x4.rotonto	get 4x4 Transformation matrix
getTrafoRotaxis	compute a 4x4 Transformation matrix for rotation around an arbitrary axis
getVisibleVertices	find vertices visible from a given viewpoints
groupPCA	Perform PCA based of the group means' covariance matrix

-- H --

histGroup

plot histogram for multiple groups.

-- I --

icpmat	match two landmark configurations using iteratively closest point search
invertFaces	invert faces' orientation of triangular mesh

-- K --

kendalldist

Calculates the Riemannian distance between two superimposed landmark configs.

-- L --

line2plane	get intersection between a line and a plane
lineplot	plot lines between landmarks
list2array	converts a list of matrices to an array
longnose.lm	landmarks and a triangular mesh representing a human nose
LPS2RAS	convert data from LPS to RAS space and back

-- M --

mcNNindex	find nearest neighbours for 2D and 3D point clouds
mergeMeshes	merge multiple triangular meshes into a single one
mesh2grey	convert a colored mesh to greyscale.
mesh2obj	export mesh objects to disk
mesh2ply	export mesh objects to disk
meshcube	calculate the corners of a mesh's bouning box
meshDist	calculates and visualises distances between surface meshes or 3D coordinates and a surface mesh.
meshDist.matrix	calculates and visualises distances between surface meshes or 3D coordinates and a surface mesh.
meshDist.mesh3d	calculates and visualises distances between surface meshes or 3D coordinates and a surface mesh.
meshPlaneIntersect	get intersections between mesh and a plane
meshres	calculate average edge length of a triangular mesh
mirror	mirror landmarks or triangular mesh in place
mirror.matrix	mirror landmarks or triangular mesh in place
mirror.mesh3d	mirror landmarks or triangular mesh in place
mirror2plane	mirror points or mesh on an arbitrary plane
mirror2plane.matrix	mirror points or mesh on an arbitrary plane
mirror2plane.mesh3d	mirror points or mesh on an arbitrary plane
Morpho	A toolbox providing methods for data-acquisition, visualisation and statistical methods related to Geometric Morphometrics and shape analysis

-- N --

name2factor	extract data from array names
name2num	extract data from array names
NNshapeReg	Estimate the shape by averaging the shape of the nearest neighbours.
nose	landmarks and a triangular mesh representing a human nose

-- O --

obj2mesh

Import 3D surface mesh files

-- P --

pcAlign	align two 3D-pointclouds/meshes by their principal axes
pcAlign.matrix	align two 3D-pointclouds/meshes by their principal axes
pcAlign.mesh3d	align two 3D-pointclouds/meshes by their principal axes
pcaplot3d	visualization of shape variation
pcaplot3d.nosymproc	visualization of shape variation
pcaplot3d.symproc	visualization of shape variation
PCdist	correlation between a reduced space and the original space
permudist	performs permutation testing for group differences.
permuvec	perfom permutation testing on angles and distances between subgroups of two major groups.
placePatch	Project semi-landmarks from a predefined atlas onto all specimen in a sample
plot.slider3d	plot the result of slider3d
plotAtlas	visualize an atlas defined by createAtlas
plotNormals	plots the normals of a triangular surface mesh.
pls2B	Two-Block partial least square regression.
plsCoVar	Get the shape changes from pls2B associated with each latent variable
plsCoVarCommonShape	Compute the shape changes along the common axis of deformations
ply2mesh	Import 3D surface mesh files
points2plane	projects a 3D coordinate orthogonally onto a plane
prcompfast	fast Principal Component Analysis (PCA)
predict.bgPCA	Compute between-group-PC scores from new data
predict.CVA	Compute CV-scores from new data
predictPLSfromData	predict 2 Block-PLS from new data
predictPLSfromScores	predict data from 2-Block PLS-scores
predictRelWarps	predict relative warps for data not included in the training data set
predictShape.lm	Predict shapes based on linear models calculated from PCscores
proc.weight	calculate weights inverse to the distances from the specified observation.
procAOVsym	Procrustes ANOVA for structures with object symmetry
ProcGPA	Workhorse function for procSym, responsible for Procrustes registration
procSym	Procrustes registration
projRead	Project points onto the closest point on a mesh

-- Q --

qqmat	Q-Q plot to assess normality of data
quad2trimesh	converts a mesh containing quadrangular faces into one only consisting of triangles

-- R --

r2morphoj	Export data to MorphoJ and Morphologika
r2morphologika	Export data to MorphoJ and Morphologika
ray2mesh	projects the vertices of a mesh along its normals onto the surface of another one.
read.csv.folder	batch import data from files
read.fcsv	read fiducials from slicer4
read.lmdta	read dta files
read.mpp	Read saved pick-points from meshlab
read.pts	reads pts files
read.slicerjson	read Landmarks from Slicer in Json format
readallTPS	Import landmarks and outlines from TPS files
readLandmarks.csv	import landmark data from csv files
regdist	correlation between shape space and tangent space
RegScore	calulate regression scores for linear model
relaxLM	relax one specific landmark configuration against a reference
relaxLM.matrix	relax one specific landmark configuration against a reference
relaxLM.mesh3d	relax one specific landmark configuration against a reference
relWarps	calculate relative Warp analysis
render	plot or save the results of meshDist
render.matrixDist	plot or save the results of meshDist
render.meshDist	plot or save the results of meshDist
resampleCurve	Resample a curve equidistantly
restoreFromPCA	restore original data from PCA
restoreShapes	restore shapes from PC-Scores or similar projections
retroDeform3d	symmetrize a bilateral landmark configuration
retroDeformMesh	symmetrize a triangular mesh
rmUnrefVertex	some little helpers for vertex operations on triangular meshes
rmVertex	some little helpers for vertex operations on triangular meshes
rotaxis3d	Rotate an object (matrix or mesh) around an arbitrary axis in 3D
rotaxis3d.matrix	Rotate an object (matrix or mesh) around an arbitrary axis in 3D
rotaxis3d.mesh3d	Rotate an object (matrix or mesh) around an arbitrary axis in 3D
rotaxisMat	calculate a rotation matrix around an arbitrary axis through the origin in 3D
rotmesh.onto	rotate ,scale and translate a mesh based on landmark information.
rotonmat	rotate matrix of landmarks
rotonto	rotates, translates and scales one matrix onto an other using Procrustes fitting
rotreverse	rotates, translates and scales one matrix onto an other using Procrustes fitting
rotreverse.matrix	rotates, translates and scales one matrix onto an other using Procrustes fitting
rotreverse.mesh3d	rotates, translates and scales one matrix onto an other using Procrustes fitting

-- S --

scalemesh	scale a mesh of class "mesh3d"
shortnose.lm	landmarks and a triangular mesh representing a human nose
shortnose.mesh	landmarks and a triangular mesh representing a human nose
skin1	predefined colors for bone and skin
skin2	predefined colors for bone and skin
skin3	predefined colors for bone and skin
skin4	predefined colors for bone and skin
skull_0144_ch_fe.mesh	Landmarks and a triangular mesh
slider2d	slides Semilandmarks along curves 2D by minimising bending energy of a thin-plate spline deformation.
slider3d	slides Semilandmarks along curves and surfaces in 3D by minimising bending energy of a thin-plate spline deformation.
solutionSpace	returns the solution space (basis and translation vector) for an equation system
sortCurve	sort curvepoints by using the subsequent neighbours
symmetrize	create a perfectly symmetric version of landmarks

-- T --

tangentPlane	calculate the orthogonal complement of a 3D-vector
tps2d	thin plate spline mapping (2D and 3D) for coordinates and triangular meshes
tps3d	thin plate spline mapping (2D and 3D) for coordinates and triangular meshes
typprob	calculate typicality probabilities
typprobClass	calculate typicality probabilities

-- U --

unrefVertex	some little helpers for vertex operations on triangular meshes
updateIndices	update a vector of indices after removal of some referenced items
updateNormals	Compute face or vertex normals of a triangular mesh

-- V --

vecx	convert an 3D array into a matrix and back
vert2points	some little helpers for vertex operations on triangular meshes
virtualMeshScan	remove all parts of a triangular mesh, not visible from a set of viewpoints

-- W --

warpmovie2d	Creates a sequence of images showing predefined steps of warping two meshes or landmark configurations (2D and 3D) into each other
warpmovie3d	Creates a sequence of images showing predefined steps of warping two meshes or landmark configurations (2D and 3D) into each other
warpmovie3d.matrix	Creates a sequence of images showing predefined steps of warping two meshes or landmark configurations (2D and 3D) into each other
warpmovie3d.mesh3d	Creates a sequence of images showing predefined steps of warping two meshes or landmark configurations (2D and 3D) into each other
write.fcsv	write fiducials in slicer4 format
write.pts	exports a matrix containing landmarks into .pts format
write.slicerjson	Export landmarks (or any 3D coordinates) to the new slicer json format