Man pages for Morpho
Calculations and Visualisations Related to Geometric Morphometrics

align2procSymalign new data to an existing Procrustes registration
angle.calccalculate angle between two vectors
angleTestTest whether the direction of two vectors is similar
anonymizeReplace ID-strings of data and associated files.
applyTransformapply affine transformation to data
areaSpherecompute the area of an n-dimensional hypersphere
areaSpherePartcompute the area of an n-dimensional hypersphere cap
armaGinvcalculate Pseudo-inverse of a Matrix using RcppArmadillo
array2listreverts list2array, converting an array to a list of matrices
arrMean3calculate mean of an array
asymPermuteAssess differences in amount and direction of asymmetric...
barycentercalculates the barycenters for all faces of a triangular mesh
bindArrconcatenate multiple arrays/matrices
boneDataLandmarks and a triangular mesh
CACcalculate common allometric component
cExtractextract information about fixed landmarks, curves and patches...
checkLMVisually browse through a sample rendering its landmarks and...
checkNAcheck for NA values in a matrix (of landmarks)
classifyclassify specimen based on between-group PCA or CVA or...
closemeshKDProject coordinates onto a target triangular surface mesh.
colorspredefined colors for bone and skin
computeAreaCompute area enclosed within an irregular polygon
computeTransformcalculate an affine transformation matrix
covDistcalculates distances and PC-coordinates of covariance...
covWcalculate the pooled within groups covariance matrix
createAtlasCreate an atlas needed in placePatch
CreateLCreate Matrices necessary for Thin-Plate Spline
createMissingListcreate a list with empty entries to be used as missingList in...
cSizecalculate Centroid Size for a landmark configuration
cutMeshPlanecut a mesh by a hyperplane and remove parts above/below that...
cutSpaceseparate a 3D-pointcloud by a hyperplane
CVACanonical Variate Analysis
data2platoniccreates 3D shapes from data to be saved as triangular meshes
deformGrid2dvisualise differences between two superimposed sets of 2D...
deformGrid3dvisualise differences between two superimposed sets of 3D...
equidistantCurvemake a curve equidistant (optionally up/downsampling)
exVarcalculate variance of a distribution stemming from prediction...
fastKmeansfast kmeans clustering for 2D or 3D point clouds
find.outliersGraphical interface to find outliers and/or to switch...
fixLMmirrorestimate missing landmarks from their bilateral counterparts
fixLMtpsestimate missing landmarks
getFacesfind indices of faces that contain specified vertices
getMeaningfulPCsget number of meaningful Principal components
getOuterViewpointsGet viewpoints on a sphere around a 3D mesh
getPCscoresObtain PC-scores for new landmark data
getPCtoldetermine the minimum ratio for two subsequent eigenvalues to...
getPLSCommonShapeGet the linear combinations associated with the common shape...
getPLSfromScorescompute changes associated with 2-Block PLS-scores
getPLSscorescompute 2-Block PLS scores for new data
getPointAlongOutlineGet a point along a line with a given distance from the start...
getSidestry to identify bilateral landmarks and sort them by side
getTrafo4x4get 4x4 Transformation matrix
getTrafoRotaxiscompute a 4x4 Transformation matrix for rotation around an...
getVisibleVerticesfind vertices visible from a given viewpoints
groupPCAPerform PCA based of the group means' covariance matrix
histGroupplot histogram for multiple groups.
icpmatmatch two landmark configurations using iteratively closest...
invertFacesinvert faces' orientation of triangular mesh
kendalldistCalculates the Riemannian distance between two superimposed...
line2planeget intersection between a line and a plane
lineplotplot lines between landmarks
list2arrayconverts a list of matrices to an array
LPS2RASconvert data from LPS to RAS space and back
mcNNindexfind nearest neighbours for 2D and 3D point clouds
mergeMeshesmerge multiple triangular meshes into a single one
mesh2greyconvert a colored mesh to greyscale.
mesh2plyexport mesh objects to disk
meshcubecalculate the corners of a mesh's bouning box
meshDistcalculates and visualises distances between surface meshes or...
meshPlaneIntersectget intersections between mesh and a plane
meshrescalculate average edge length of a triangular mesh
mirrormirror landmarks or triangular mesh in place
mirror2planemirror points or mesh on an arbitrary plane
Morpho-deprecateddeprecated functions of Morpho
Morpho-packageA toolbox providing methods for data-acquisition,...
name2factorextract data from array names
NNshapeRegEstimate the shape by averaging the shape of the nearest...
noselandmarks and a triangular mesh representing a human nose
pcAlignalign two 3D-pointclouds/meshes by their principal axes
pcaplot3dvisualization of shape variation
PCdistcorrelation between a reduced space and the original space
permudistperforms permutation testing for group differences.
permuvecperfom permutation testing on angles and distances between...
placePatchProject semi-landmarks from a predefined atlas onto all...
plotAtlasvisualize an atlas defined by createAtlas
plotNormalsplots the normals of a triangular surface mesh.
plot.slider3dplot the result of slider3d
pls2BTwo-Block partial least square regression.
plsCoVarGet the shape changes from pls2B associated with each latent...
plsCoVarCommonShapeCompute the shape changes along the common axis of...
ply2meshImport 3D surface mesh files
points2planeprojects a 3D coordinate orthogonally onto a plane
prcompfastfast Principal Component Analysis (PCA)
predict.bgPCACompute between-group-PC scores from new data
predict.CVACompute CV-scores from new data
predictPLSfromDatapredict 2 Block-PLS from new data
predictPLSfromScorespredict data from 2-Block PLS-scores
predictRelWarpspredict relative warps for data not included in the training...
predictShape.lmPredict shapes based on linear models calculated from...
procAOVsymProcrustes ANOVA for structures with object symmetry
ProcGPAWorkhorse function for procSym, responsible for Procrustes...
procSymProcrustes registration
proc.weightcalculate weights inverse to the distances from the specified...
projReadProject points onto the closest point on a mesh
qqmatQ-Q plot to assess normality of data
quad2trimeshconverts a mesh containing quadrangular faces into one only...
r2morphojExport data to MorphoJ and Morphologika
ray2meshprojects the vertices of a mesh along its normals onto the...
readallTPSImport landmarks and outlines from TPS files
read.csv.folderbatch import data from files
read.fcsvread fiducials from slicer4
readLandmarks.csvimport landmark data from csv files
read.lmdtaread dta files
read.mppRead saved pick-points from meshlab
read.ptsreads pts files
read.slicerjsonread Landmarks from Slicer in Json format
regdistcorrelation between shape space and tangent space
RegScorecalulate regression scores for linear model
relaxLMrelax one specific landmark configuration against a reference
relWarpscalculate relative Warp analysis
renderplot or save the results of meshDist
resampleCurveResample a curve equidistantly
restoreFromPCArestore original data from PCA
restoreShapesrestore shapes from PC-Scores or similar projections
retroDeform3dsymmetrize a bilateral landmark configuration
retroDeformMeshsymmetrize a triangular mesh
rotaxis3dRotate an object (matrix or mesh) around an arbitrary axis in...
rotaxisMatcalculate a rotation matrix around an arbitrary axis through...
rotmesh.ontorotate ,scale and translate a mesh based on landmark...
rotonmatrotate matrix of landmarks
rotontorotates, translates and scales one matrix onto an other using...
scalemeshscale a mesh of class "mesh3d"
slider2dslides Semilandmarks along curves 2D by minimising bending...
slider3dslides Semilandmarks along curves and surfaces in 3D by...
solutionSpacereturns the solution space (basis and translation vector) for...
sortCurvesort curvepoints by using the subsequent neighbours
symmetrizecreate a perfectly symmetric version of landmarks
tangentPlanecalculate the orthogonal complement of a 3D-vector
tps3dthin plate spline mapping (2D and 3D) for coordinates and...
typprobcalculate typicality probabilities
updateIndicesupdate a vector of indices after removal of some referenced...
updateNormalsCompute face or vertex normals of a triangular mesh
vecxconvert an 3D array into a matrix and back
vertexsome little helpers for vertex operations on triangular...
virtualMeshScanremove all parts of a triangular mesh, not visible from a set...
warpmovie3dCreates a sequence of images showing predefined steps of...
write.fcsvwrite fiducials in slicer4 format
write.ptsexports a matrix containing landmarks into .pts format
write.slicerjsonExport landmarks (or any 3D coordinates) to the new slicer...
Morpho documentation built on Feb. 16, 2023, 10:51 p.m.