CAC                     calculate common allometric component
CVA                     Canonical Variate Analysis
CreateL                 Create Matrices necessary for Thin-Plate Spline
Morpho-package          A toolbox providing methods for
                        data-acquisitiopn, 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
angle.calc              calculate angle between two vectors
anonymize               Replace ID-strings of data and associated
                        files.
applyTransform          apply affine transformation to data
arrMean3                calculate mean of an array
asymPermute             Assess differences in amount and direction of
                        asymmetric variation
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.
classify                classify specimen based on between-group PCA or
                        CVA
closemeshKD             Project coordinates onto a target triangular
                        surface mesh.
colors                  predefined colors for bone and skin
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
deformGrid2d            visualise differences between two superimposed
                        sets of 2D landmarks
deformGrid3d            visualise differences between two superimposed
                        sets of 3D landmarks
exVar                   calculate variance of a distribution stemming
                        from prediction models
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
getTrafo4x4             get 4x4 Transformation matrix
getTrafoRotaxis         compute a 4x4 Transformation matrix for
                        rotation around an arbitrary axis
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
invertFaces             invert faces' orientation of triangular mesh
kendalldist             Calculates the Riemannian distance between two
                        superimposed landmark configs.
lineplot                plot lines between landmarks
mcNNindex               find nearest neighbours for point clouds
meanMat                 fast calculation of a Matrix' per row/ per
                        column mean - useful for very large matrices
mergeMeshes             merge multiple triangular meshes into a single
                        one
mesh2grey               convert a colored mesh to greyscale.
mesh2obj                export mesh objects to disk
meshDist.matrix         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
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
plotAtlas               visualize an atlas defined by createAtlas
plotNormals             plots the normals of a triangular surface mesh.
pls2B                   Two-Block partial least square regression.
points2plane            projects a 3D coordinate orthogonally onto a
                        plane
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.lmdta              read dta files
read.mpp                Read saved pick-points from meshlab
read.pts                reads pts files
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.matrixDist       plot or save the results of meshDist
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"
showPC                  convert PCs to landmark configuration
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
symmetrize              create a perfectly symmetric version of
                        landmarks
tps3d                   thin plate spline mapping
typprob                 calculate typicality probabilities
unrefVertex             some little helpers for vertex operations on
                        triangular meshes
updateNormals           Compute face or vertex normals of a triangular
                        mesh
vecx                    convert an 3D array into a matrix and back
warp.mesh               warping a mesh onto another configuration
warpmovie3d             Creates a sequence of images showing predefined
                        steps of warping two meshes or landmark
                        configurations (2D and 3D) into each other
write.pts               exports a matrix containing landmarks into .pts
                        format
