A toolset for Geometric Morphometrics and mesh processing. This includes (among other stuff) mesh deformations based on reference points, permutation tests, detection of outliers, processing of sliding semi-landmarks and semi-automated surface landmark placement.
|Author||Stefan Schlager [aut, cre, cph], Gregory Jefferis [ctb]|
|Date of publication||2016-09-13 12:10:26|
|Maintainer||Stefan Schlager <firstname.lastname@example.org>|
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