| 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 |
| 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... |
| barycenter | calculates the barycenters for all faces of a triangular mesh |
| bindArr | concatenate multiple arrays/matrices |
| boneData | Landmarks and a triangular mesh |
| CAC | calculate common allometric component |
| cExtract | extract information about fixed landmarks, curves and patches... |
| checkLM | Visually browse through a sample rendering its landmarks and... |
| checkNA | check for NA values in a matrix (of landmarks) |
| classify | classify specimen based on between-group PCA or CVA or... |
| 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... |
| 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... |
| cSize | calculate Centroid Size for a landmark configuration |
| cutMeshPlane | cut a mesh by a hyperplane and remove parts above/below that... |
| cutSpace | separate a 3D-pointcloud by a hyperplane |
| CVA | Canonical Variate Analysis |
| data2platonic | creates 3D shapes from data to be saved as triangular meshes |
| deformGrid2d | visualise differences between two superimposed sets of 2D... |
| deformGrid3d | visualise differences between two superimposed sets of 3D... |
| equidistantCurve | make a curve equidistant (optionally up/downsampling) |
| exVar | calculate variance of a distribution stemming from prediction... |
| fastKmeans | fast kmeans clustering for 2D or 3D point clouds |
| find.outliers | Graphical interface to find outliers and/or to switch... |
| 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... |
| getPLSCommonShape | Get the linear combinations associated with the common shape... |
| 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... |
| 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... |
| 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... |
| invertFaces | invert faces' orientation of triangular mesh |
| kendalldist | Calculates the Riemannian distance between two superimposed... |
| line2plane | get intersection between a line and a plane |
| lineplot | plot lines between landmarks |
| list2array | converts a list of matrices to an array |
| LPS2RAS | convert data from LPS to RAS space and back |
| 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. |
| 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... |
| 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 |
| mirror2plane | mirror points or mesh on an arbitrary plane |
| Morpho-deprecated | deprecated functions of Morpho |
| Morpho-package | A toolbox providing methods for data-acquisition,... |
| name2factor | extract data from array names |
| NNshapeReg | Estimate the shape by averaging the shape of the nearest... |
| 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 |
| 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... |
| placePatch | Project semi-landmarks from a predefined atlas onto all... |
| plotAtlas | visualize an atlas defined by createAtlas |
| plotNormals | plots the normals of a triangular surface mesh. |
| plot.slider3d | plot the result of slider3d |
| pls2B | Two-Block partial least square regression. |
| plsCoVar | Get the shape changes from pls2B associated with each latent... |
| plsCoVarCommonShape | Compute the shape changes along the common axis of... |
| 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... |
| predictShape.lm | Predict shapes based on linear models calculated from... |
| procAOVsym | Procrustes ANOVA for structures with object symmetry |
| ProcGPA | Workhorse function for procSym, responsible for Procrustes... |
| procSym | Procrustes registration |
| proc.weight | calculate weights inverse to the distances from the specified... |
| 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... |
| r2morphoj | Export data to MorphoJ and Morphologika |
| ray2mesh | projects the vertices of a mesh along its normals onto the... |
| readallTPS | Import landmarks and outlines from TPS files |
| read.csv.folder | batch import data from files |
| read.fcsv | read fiducials from slicer4 |
| readLandmarks.csv | import landmark data from csv files |
| 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 |
| regdist | correlation between shape space and tangent space |
| RegScore | calulate regression scores for linear model |
| relaxLM | relax one specific landmark configuration against a reference |
| relWarps | calculate relative Warp analysis |
| 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... |
| rotaxisMat | calculate a rotation matrix around an arbitrary axis through... |
| rotmesh.onto | rotate ,scale and translate a mesh based on landmark... |
| rotonmat | rotate matrix of landmarks |
| rotonto | rotates, translates and scales one matrix onto an other using... |
| scalemesh | scale a mesh of class "mesh3d" |
| slider2d | slides Semilandmarks along curves 2D by minimising bending... |
| slider3d | slides Semilandmarks along curves and surfaces in 3D by... |
| solutionSpace | returns the solution space (basis and translation vector) for... |
| sortCurve | sort curvepoints by using the subsequent neighbours |
| symmetrize | create a perfectly symmetric version of landmarks |
| tangentPlane | calculate the orthogonal complement of a 3D-vector |
| tps3d | thin plate spline mapping (2D and 3D) for coordinates and... |
| typprob | calculate typicality probabilities |
| updateIndices | update a vector of indices after removal of some referenced... |
| updateNormals | Compute face or vertex normals of a triangular mesh |
| vecx | convert an 3D array into a matrix and back |
| vertex | some little helpers for vertex operations on triangular... |
| virtualMeshScan | remove all parts of a triangular mesh, not visible from a set... |
| warpmovie3d | Creates a sequence of images showing predefined steps of... |
| 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... |
