A B C D E F G H I K L M N O P Q R S T U V W
Morpho-package | A toolbox providing methods for data-acquisition, visualisation and statistical methods related to Geometric Morphometrics and shape analysis |
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 |
applyTransform.default | apply affine transformation to data |
applyTransform.matrix | apply affine transformation to data |
applyTransform.mesh3d | 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 variation (only object symmetry) |
barycenter | calculates the barycenters for all faces of a triangular mesh |
bindArr | concatenate multiple arrays/matrices |
bone1 | predefined colors for bone and skin |
bone2 | predefined colors for bone and skin |
bone3 | predefined colors for bone and skin |
boneData | Landmarks and a triangular mesh |
boneLM | Landmarks and a triangular mesh |
CAC | calculate common allometric component |
cExtract | extract information about fixed landmarks, curves and patches from and atlas generated by "landmark" |
checkLM | Visually browse through a sample rendering its landmarks and corresponding surfaces. |
checkNA | check for NA values in a matrix (of landmarks) |
classify | classify specimen based on between-group PCA or CVA or typprobClass |
classify.bgPCA | classify specimen based on between-group PCA or CVA or typprobClass |
classify.CVA | classify specimen based on between-group PCA or CVA or typprobClass |
classify.typprob | classify specimen based on between-group PCA or CVA or typprobClass |
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 matrices |
covPCA | calculates distances and PC-coordinates of covariance matrices |
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 slider3d |
crossProduct | calculate the orthogonal complement of a 3D-vector |
cSize | calculate Centroid Size for a landmark configuration |
cutMeshPlane | cut a mesh by a hyperplane and remove parts above/below that plane |
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 landmarks |
deformGrid3d | visualise differences between two superimposed sets of 3D landmarks |
equidistantCurve | make a curve equidistant (optionally up/downsampling) |
export | plot or save the results of meshDist |
export.meshDist | plot or save the results of meshDist |
exVar | calculate variance of a distribution stemming from prediction models |
exVar.lm | calculate variance of a distribution stemming from prediction models |
exVar.mvr | calculate variance of a distribution stemming from prediction models |
facenormals | Compute face or vertex normals of a triangular mesh |
fastKmeans | fast kmeans clustering for 2D or 3D point clouds |
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 |
fixLMmirror.array | estimate missing landmarks from their bilateral counterparts |
fixLMmirror.matrix | 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 be considered different |
getPLSCommonShape | Get the linear combinations associated with the common shape change in each latent dimension of a pls2B |
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 of the line |
getSides | try to identify bilateral landmarks and sort them by side |
getTrafo4x4 | get 4x4 Transformation matrix |
getTrafo4x4.rotonto | get 4x4 Transformation matrix |
getTrafoRotaxis | compute a 4x4 Transformation matrix for rotation around an arbitrary axis |
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 point search |
invertFaces | invert faces' orientation of triangular mesh |
kendalldist | Calculates the Riemannian distance between two superimposed landmark configs. |
line2plane | get intersection between a line and a plane |
lineplot | plot lines between landmarks |
list2array | converts a list of matrices to an array |
longnose.lm | landmarks and a triangular mesh representing a human nose |
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. |
mesh2obj | export mesh objects to disk |
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 3D coordinates and a surface mesh. |
meshDist.matrix | calculates and visualises distances between surface meshes or 3D coordinates and a surface mesh. |
meshDist.mesh3d | calculates and visualises distances between surface meshes or 3D coordinates and a surface mesh. |
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 |
mirror.matrix | mirror landmarks or triangular mesh in place |
mirror.mesh3d | mirror landmarks or triangular mesh in place |
mirror2plane | mirror points or mesh on an arbitrary plane |
mirror2plane.matrix | mirror points or mesh on an arbitrary plane |
mirror2plane.mesh3d | mirror points or mesh on an arbitrary plane |
Morpho | A toolbox providing methods for data-acquisition, visualisation and statistical methods related to Geometric Morphometrics and shape analysis |
name2factor | extract data from array names |
name2num | extract data from array names |
NNshapeReg | Estimate the shape by averaging the shape of the nearest neighbours. |
nose | landmarks and a triangular mesh representing a human nose |
obj2mesh | Import 3D surface mesh files |
pcAlign | align two 3D-pointclouds/meshes by their principal axes |
pcAlign.matrix | align two 3D-pointclouds/meshes by their principal axes |
pcAlign.mesh3d | align two 3D-pointclouds/meshes by their principal axes |
pcaplot3d | visualization of shape variation |
pcaplot3d.nosymproc | visualization of shape variation |
pcaplot3d.symproc | 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 subgroups of two major groups. |
placePatch | Project semi-landmarks from a predefined atlas onto all specimen in a sample |
plot.slider3d | plot the result of slider3d |
plotAtlas | visualize an atlas defined by createAtlas |
plotNormals | plots the normals of a triangular surface mesh. |
pls2B | Two-Block partial least square regression. |
plsCoVar | Get the shape changes from pls2B associated with each latent variable |
plsCoVarCommonShape | Compute the shape changes along the common axis of deformations |
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 data set |
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 |
ProcGPA | Workhorse function for procSym, responsible for Procrustes registration |
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 |
r2morphologika | 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.fcsv | read fiducials from slicer4 |
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 |
readallTPS | Import landmarks and outlines from TPS files |
readLandmarks.csv | import landmark data from csv 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 |
relaxLM.matrix | relax one specific landmark configuration against a reference |
relaxLM.mesh3d | relax one specific landmark configuration against a reference |
relWarps | calculate relative Warp analysis |
render | plot or save the results of meshDist |
render.matrixDist | plot or save the results of meshDist |
render.meshDist | 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 |
rmUnrefVertex | some little helpers for vertex operations on triangular meshes |
rmVertex | some little helpers for vertex operations on triangular meshes |
rotaxis3d | Rotate an object (matrix or mesh) around an arbitrary axis in 3D |
rotaxis3d.matrix | Rotate an object (matrix or mesh) around an arbitrary axis in 3D |
rotaxis3d.mesh3d | 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 |
rotreverse | rotates, translates and scales one matrix onto an other using Procrustes fitting |
rotreverse.matrix | rotates, translates and scales one matrix onto an other using Procrustes fitting |
rotreverse.mesh3d | rotates, translates and scales one matrix onto an other using Procrustes fitting |
scalemesh | scale a mesh of class "mesh3d" |
shortnose.lm | landmarks and a triangular mesh representing a human nose |
shortnose.mesh | landmarks and a triangular mesh representing a human nose |
skin1 | predefined colors for bone and skin |
skin2 | predefined colors for bone and skin |
skin3 | predefined colors for bone and skin |
skin4 | predefined colors for bone and skin |
skull_0144_ch_fe.mesh | Landmarks and a triangular mesh |
slider2d | slides Semilandmarks along curves 2D by minimising bending energy of a thin-plate spline deformation. |
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 |
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 |
tps2d | thin plate spline mapping (2D and 3D) for coordinates and triangular meshes |
tps3d | thin plate spline mapping (2D and 3D) for coordinates and triangular meshes |
typprob | calculate typicality probabilities |
typprobClass | calculate typicality probabilities |
unrefVertex | some little helpers for vertex operations on triangular meshes |
updateIndices | update a vector of indices after removal of some referenced items |
updateNormals | Compute face or vertex normals of a triangular mesh |
vecx | convert an 3D array into a matrix and back |
vert2points | some little helpers for vertex operations on triangular meshes |
virtualMeshScan | remove all parts of a triangular mesh, not visible from a set of viewpoints |
warpmovie2d | Creates a sequence of images showing predefined steps of warping two meshes or landmark configurations (2D and 3D) into each other |
warpmovie3d | Creates a sequence of images showing predefined steps of warping two meshes or landmark configurations (2D and 3D) into each other |
warpmovie3d.matrix | Creates a sequence of images showing predefined steps of warping two meshes or landmark configurations (2D and 3D) into each other |
warpmovie3d.mesh3d | Creates a sequence of images showing predefined steps of warping two meshes or landmark configurations (2D and 3D) into each other |
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 json format |