Morpho: Calculations and Visualisations Related to Geometric Morphometrics

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 <stefan.schlager@uniklinik-freiburg.de>
License
GPL-2
Version
2.4.1.1
URLs

View on CRAN

Man pages

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

Files in this package

Morpho
Morpho/inst
Morpho/inst/NEWS.Rd
Morpho/inst/COPYRIGHTS
Morpho/inst/extdata
Morpho/inst/extdata/SCP1.ply
Morpho/inst/extdata/landmarks.pts
Morpho/tests
Morpho/tests/testthat.R
Morpho/tests/testthat
Morpho/tests/testthat/test-pls2B.r
Morpho/tests/testthat/test-mirror.r
Morpho/tests/testthat/test-relWarps.r
Morpho/tests/testthat/test-CVA.r
Morpho/tests/testthat/testdata
Morpho/tests/testthat/testdata/slider3d.rds
Morpho/tests/testthat/testdata/skullMir.rds
Morpho/tests/testthat/testdata/CVA.rds
Morpho/tests/testthat/testdata/pls-baseline.rds
Morpho/tests/testthat/testdata/rW.rds
Morpho/tests/testthat/test-slider3d.r
Morpho/src
Morpho/src/points2mesh.h
Morpho/src/permudistArma.h
Morpho/src/Makevars
Morpho/src/permudistArma.cpp
Morpho/src/tpsfx.cpp
Morpho/src/tweakU.cpp
Morpho/src/edgePlane.cpp
Morpho/src/asymPerm.cpp
Morpho/src/CubeStuff.h
Morpho/src/ang_calc.cpp
Morpho/src/armaGinv.h
Morpho/src/CubeStuff.cpp
Morpho/src/meshres.cpp
Morpho/src/doozers.h
Morpho/src/fastSubsetMeans.cpp
Morpho/src/asymPerm.h
Morpho/src/covPCA.cpp
Morpho/src/doozers.cpp
Morpho/src/points2mesh.cpp
Morpho/src/updateNormals.cpp
Morpho/src/barycenter.cpp
Morpho/src/addCube.h
Morpho/src/CVAdists.cpp
Morpho/src/armaGinv.cpp
Morpho/src/covPCA.h
Morpho/src/createL.cpp
Morpho/src/updateNormals.h
Morpho/src/face_zero.cpp
Morpho/src/CVAdists.h
Morpho/NAMESPACE
Morpho/data
Morpho/data/datalist
Morpho/data/nose.rda
Morpho/data/boneData.rda
Morpho/R
Morpho/R/procAOVsym.r
Morpho/R/typprob.r
Morpho/R/deformGrid2d.r
Morpho/R/difplot.lm.r
Morpho/R/closemeshKD.r
Morpho/R/plot.normals.r
Morpho/R/relwarps.r
Morpho/R/relax.lm.r
Morpho/R/armaGinv.r
Morpho/R/ProcGPA.r
Morpho/R/applyTransform.r
Morpho/R/Semislide.r
Morpho/R/line2plane.r
Morpho/R/cSize.r
Morpho/R/projRead.r
Morpho/R/scaleproc.r
Morpho/R/vecx.r
Morpho/R/solutionSpace.r
Morpho/R/mergeMeshes.r
Morpho/R/readallTPS.r
Morpho/R/list2array.r
Morpho/R/CVAdists.r
Morpho/R/name2.r
Morpho/R/obj2mesh.r
Morpho/R/regdist.raw.r
Morpho/R/eigenPCA.r
Morpho/R/read.pts.r
Morpho/R/meshcube.r
Morpho/R/histGroup.r
Morpho/R/createVarTable.r
Morpho/R/points2plane.r
Morpho/R/showPC.r
Morpho/R/calcTang_U.r
Morpho/R/CVA.crova.r
Morpho/R/classify.r
Morpho/R/write.pts.r
Morpho/R/PCmeaning.r
Morpho/R/orp.r
Morpho/R/asymPermu.r
Morpho/R/addo.r
Morpho/R/meshDist.r
Morpho/R/pcaplot3d.r
Morpho/R/deform.grid.r
Morpho/R/meshPlaneIntersect.r
Morpho/R/prcompfast.r
Morpho/R/tanplan.r
Morpho/R/place.patch.r
Morpho/R/angle.calc.r
Morpho/R/onUnload.r
Morpho/R/difplot.lm2D.r
Morpho/R/groupPCA.r
Morpho/R/fiducials.r
Morpho/R/calcGamma.r
Morpho/R/barycenter.r
Morpho/R/createMissingList.r
Morpho/R/groupPCAcrova.r
Morpho/R/calcTang_U_s.r
Morpho/R/equidistantCurve.r
Morpho/R/rotmesh.onto.r
Morpho/R/rotonmat.r
Morpho/R/mirror.r
Morpho/R/cutSpace.r
Morpho/R/quad2trimesh.r
Morpho/R/mesh2grey.r
Morpho/R/lineplot.r
Morpho/R/vertex.r
Morpho/R/meshDistZExport.r
Morpho/R/check.lm.r
Morpho/R/meshDistMatrix.r
Morpho/R/ray2mesh.r
Morpho/R/read.mpp.r
Morpho/R/ply2mesh.r
Morpho/R/meshres.r
Morpho/R/permudist.r
Morpho/R/file2mesh.r
Morpho/R/CAC.r
Morpho/R/pls2B.r
Morpho/R/ignoreNA.r
Morpho/R/permuvec.r
Morpho/R/proc.weight.r
Morpho/R/r2morphoj.r
Morpho/R/r2morphologika.r
Morpho/R/warpmovie.matrix.r
Morpho/R/colors.r
Morpho/R/gdif.r
Morpho/R/anonymize.r
Morpho/R/NNshapeReg.r
Morpho/R/Atlas.r
Morpho/R/CreateL.r
Morpho/R/fixLMtps.r
Morpho/R/fx.r
Morpho/R/PCdist.r
Morpho/R/find.outliers.r
Morpho/R/updateNormals.r
Morpho/R/fastKmeans.r
Morpho/R/mcNNindex.r
Morpho/R/mesh2ply.r
Morpho/R/RegScore.r
Morpho/R/kendalldist.r
Morpho/R/ang.r
Morpho/R/rot.proc.r
Morpho/R/covDist.r
Morpho/R/write.obj.r
Morpho/R/ComputeTransform.r
Morpho/R/tps3d.r
Morpho/R/read.lmdta.r
Morpho/R/rotaxis.r
Morpho/R/rotonto.r
Morpho/R/readLandmarks.csv.r
Morpho/R/predictShape.lm.r
Morpho/R/retrodeform.r
Morpho/R/bindArr.r
Morpho/R/crossp.r
Morpho/R/mesh2obj.r
Morpho/R/Morpho-package.R
Morpho/R/warpmovie.r
Morpho/R/read.obj.r
Morpho/R/exVar.r
Morpho/R/symmetrize.r
Morpho/R/slider3d.r
Morpho/R/pcAlign.r
Morpho/R/scalemesh.r
Morpho/R/cExtract.r
Morpho/R/angleTest.r
Morpho/R/read.csv.folder.r
Morpho/R/CVA.r
Morpho/R/conv2backf.r
Morpho/R/procSym.r
Morpho/R/qqmat.r
Morpho/R/fixLMmirror.r
Morpho/MD5
Morpho/DESCRIPTION
Morpho/man
Morpho/man/updateNormals.Rd
Morpho/man/applyTransform.Rd
Morpho/man/meshPlaneIntersect.Rd
Morpho/man/line2plane.Rd
Morpho/man/kendalldist.Rd
Morpho/man/plsCoVar.Rd
Morpho/man/CVA.Rd
Morpho/man/deformGrid2d.Rd
Morpho/man/mesh2grey.Rd
Morpho/man/areaSpherePart.Rd
Morpho/man/asymPermute.Rd
Morpho/man/quad2trimesh.Rd
Morpho/man/read.pts.Rd
Morpho/man/write.pts.Rd
Morpho/man/cutSpace.Rd
Morpho/man/solutionSpace.Rd
Morpho/man/invertFaces.Rd
Morpho/man/mirror2plane.Rd
Morpho/man/checkLM.Rd
Morpho/man/plotNormals.Rd
Morpho/man/rotaxis3d.Rd
Morpho/man/rotonmat.Rd
Morpho/man/typprob.Rd
Morpho/man/retroDeformMesh.Rd
Morpho/man/read.mpp.Rd
Morpho/man/predictShape.lm.Rd
Morpho/man/exVar.Rd
Morpho/man/rotaxisMat.Rd
Morpho/man/pcAlign.Rd
Morpho/man/mergeMeshes.Rd
Morpho/man/proc.weight.Rd
Morpho/man/ply2mesh.Rd
Morpho/man/prcompfast.Rd
Morpho/man/barycenter.Rd
Morpho/man/read.csv.folder.Rd
Morpho/man/sortCurve.Rd
Morpho/man/placePatch.Rd
Morpho/man/pcaplot3d.Rd
Morpho/man/procSym.Rd
Morpho/man/readallTPS.Rd
Morpho/man/ProcGPA.Rd
Morpho/man/armaGinv.Rd
Morpho/man/render.Rd
Morpho/man/cSize.Rd
Morpho/man/qqmat.Rd
Morpho/man/pls2B.Rd
Morpho/man/relaxLM.Rd
Morpho/man/classify.Rd
Morpho/man/predictPLSfromScores.Rd
Morpho/man/cutMeshPlane.Rd
Morpho/man/getTrafo4x4.Rd
Morpho/man/vecx.Rd
Morpho/man/r2morphoj.Rd
Morpho/man/projRead.Rd
Morpho/man/cExtract.Rd
Morpho/man/readLandmarks.csv.Rd
Morpho/man/mesh2ply.Rd
Morpho/man/Morpho-package.Rd
Morpho/man/name2factor.Rd
Morpho/man/getPLSscores.Rd
Morpho/man/find.outliers.Rd
Morpho/man/points2plane.Rd
Morpho/man/getPCtol.Rd
Morpho/man/meshDist.Rd
Morpho/man/tps3d.Rd
Morpho/man/meshcube.Rd
Morpho/man/mirror.Rd
Morpho/man/covW.Rd
Morpho/man/lineplot.Rd
Morpho/man/angleTest.Rd
Morpho/man/histGroup.Rd
Morpho/man/deformGrid3d.Rd
Morpho/man/Morpho-deprecated.Rd
Morpho/man/angle.calc.Rd
Morpho/man/showPC.Rd
Morpho/man/meshres.Rd
Morpho/man/retroDeform3d.Rd
Morpho/man/plot.slider3d.Rd
Morpho/man/read.lmdta.Rd
Morpho/man/write.fcsv.Rd
Morpho/man/list2array.Rd
Morpho/man/rotmesh.onto.Rd
Morpho/man/permuvec.Rd
Morpho/man/createMissingList.Rd
Morpho/man/equidistantCurve.Rd
Morpho/man/bindArr.Rd
Morpho/man/permudist.Rd
Morpho/man/getFaces.Rd
Morpho/man/groupPCA.Rd
Morpho/man/PCdist.Rd
Morpho/man/relWarps.Rd
Morpho/man/procAOVsym.Rd
Morpho/man/CreateL.Rd
Morpho/man/closemeshKD.Rd
Morpho/man/predictPLSfromData.Rd
Morpho/man/vertex.Rd
Morpho/man/fixLMtps.Rd
Morpho/man/mcNNindex.Rd
Morpho/man/computeTransform.Rd
Morpho/man/CAC.Rd
Morpho/man/ray2mesh.Rd
Morpho/man/rotonto.Rd
Morpho/man/boneData.Rd
Morpho/man/read.fcsv.Rd
Morpho/man/createAtlas.Rd
Morpho/man/areaSphere.Rd
Morpho/man/fixLMmirror.Rd
Morpho/man/tangentPlane.Rd
Morpho/man/warpmovie3d.Rd
Morpho/man/RegScore.Rd
Morpho/man/getPLSfromScores.Rd
Morpho/man/symmetrize.Rd
Morpho/man/scalemesh.Rd
Morpho/man/getMeaningfulPCs.Rd
Morpho/man/regdist.Rd
Morpho/man/slider3d.Rd
Morpho/man/colors.Rd
Morpho/man/NNshapeReg.Rd
Morpho/man/covDist.Rd
Morpho/man/nose.Rd
Morpho/man/fastKmeans.Rd
Morpho/man/anonymize.Rd
Morpho/man/plotAtlas.Rd
Morpho/man/icpmat.Rd
Morpho/man/getTrafoRotaxis.Rd
Morpho/man/arrMean3.Rd