Calculations and Visualisations Related to Geometric Morphometrics

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... |

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