CAC                     calculate common allometric component
CVA                     Canonical Variate Analysis
CreateL                 Create Matrices necessary for Thin-Plate Spline
ILDS                    Compute Pairwise Landmark Distances
ILDSR2                  Compute R2 for Interlandmark Distances
LPS2RAS                 convert data from LPS to RAS space and back
Morpho-package          A toolbox providing methods for
                        data-acquisition, visualisation and statistical
                        methods related to Geometric Morphometrics and
                        shape analysis
NNshapeReg              Estimate the shape by averaging the shape of
                        the nearest neighbours.
PCdist                  correlation between a reduced space and the
                        original space
ProcGPA                 Workhorse function for procSym, responsible for
                        Procrustes registration
RegScore                calulate regression scores for linear model
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
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
arrMean3                calculate mean of an array
array2list              reverts list2array, converting an array to a
                        list of matrices
asymPermute             Assess differences in amount and direction of
                        asymmetric variation (only object symmetry)
barycenter              calculates the barycenters for all faces of a
                        triangular mesh
bindArr                 concatenate multiple arrays/matrices
boneData                Landmarks and a triangular mesh
cExtract                extract information about fixed landmarks,
                        curves and patches from and atlas generated by
                        "landmark"
cSize                   calculate Centroid Size for a landmark
                        configuration
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
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
covW                    calculate the pooled within groups covariance
                        matrix
createAtlas             Create an atlas needed in placePatch
createMissingList       create a list with empty entries to be used as
                        missingList in slider3d
crossProduct            calculate the orthogonal complement of a
                        3D-vector
cutMeshPlane            cut a mesh by a hyperplane and remove parts
                        above/below that plane
cutSpace                separate a 3D-pointcloud by a hyperplane
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
equidistantCurve        make a curve equidistant (optionally
                        up/downsampling)
exVar                   calculate variance of a distribution stemming
                        from prediction models
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
fixLMtps                estimate missing landmarks
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
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
histGroup               plot histogram for multiple groups.
icpmat                  match two landmark configurations using
                        iteratively closest point search
inscribeEllipse         Inscribe the maximum ellipse into any arbitrary
                        2D polygon
inscribeEllipseRot      Inscribe the maximum ellipse into any arbitrary
                        2D polygon including rotations
invertFaces             invert faces' orientation of triangular mesh
kendalldist             Calculates the Riemannian distance between two
                        superimposed landmark configs.
line2plane              get intersection between a line and a plane
lineplot                plot lines between landmarks
list2array              converts a list of matrices to an array
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
meshDist                calculates and visualises distances between
                        surface meshes or 3D coordinates and a surface
                        mesh.
meshPlaneIntersect      get intersections between mesh and a plane
meshcube                calculate the corners of a mesh's bouning box
meshres                 calculate average edge length of a triangular
                        mesh
mirror                  mirror landmarks or triangular mesh in place
mirror2plane            mirror points or mesh on an arbitrary plane
name2factor             extract data from array names
nose                    landmarks and a triangular mesh representing a
                        human nose
pcAlign                 align two 3D-pointclouds/meshes by their
                        principal axes
pcaplot3d               visualization of shape variation
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.ILDSR2             Plot graphical report for ILDSR2
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
points2plane            projects a 3D coordinate orthogonally onto a
                        plane
prcompfast              fast Principal Component Analysis (PCA)
predict.CVA             Compute CV-scores from new data
predict.bgPCA           Compute between-group-PC 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
procSym                 Procrustes registration
projRead                Project points onto the closest point on a mesh
qqmat                   Q-Q plot to assess normality of data
quad2trimesh            converts a mesh containing quadrangular faces
                        into one only consisting of triangles
r2morphoj               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
readLandmarks.csv       import landmark data from csv files
readallTPS              Import landmarks and outlines from TPS files
regdist                 correlation between shape space and tangent
                        space
relWarps                calculate relative Warp analysis
relaxLM                 relax one specific landmark configuration
                        against a reference
render                  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
rotaxis3d               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
scalemesh               scale a mesh of class "mesh3d"
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
tps3d                   thin plate spline mapping (2D and 3D) for
                        coordinates and triangular meshes
typprob                 calculate typicality probabilities
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
vecx                    convert an 3D array into a matrix and back
virtualMeshScan         remove all parts of a triangular mesh, not
                        visible from a set of viewpoints
visualize               Plot the ILDS with the relevant ILDS ighlighted
warpmovie3d             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
