- Morpho: Calculations and Visualisations Related to Geometric Morphometrics
- read.lmdta: read dta files
read dta files
reads .dta files created by the software Landmark http://graphics.idav.ucdavis.edu/research/EvoMorph
a dta file
specifies a value that indicates missing values
array containing landmarks dimnames will be Information of ID and landmark names specified in Landmark
Information extracted from the header of the dta file
character vector containing the names of the individuals as specified in the dta file
- 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
- 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...
- 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
- 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
- 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
- getPCtol: determine the minimum ratio for two subsequent eigenvalues to...
- getPLSfromScores: compute changes associated with 2-Block PLS-scores
- getPLSscores: compute 2-Block PLS scores for new data
- getTrafo4x4: get 4x4 Transformation matrix
- getTrafoRotaxis: compute a 4x4 Transformation matrix for rotation around an...
- 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
- 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...
- ply2mesh: Import 3D surface mesh files
- points2plane: projects a 3D coordinate orthogonally onto a plane
- prcompfast: fast Principal Component Analysis (PCA)
- predictPLSfromData: predict 2 Block-PLS from new data
- predictPLSfromScores: predict data from 2-Block PLS-scores
- 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
- 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
- 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"
- showPC: convert PCs to landmark configuration
- 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
- 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...
- 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