Calculations and Visualisations Related to Geometric Morphometrics

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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

Morpho-package 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