Calculations and visualizations related to Geometric Morphometrics

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Documentation for package ‘Morpho’ version 0.23.3

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Morpho-package loads of stuff relating to Geometric Morphometrics and shape analysis
adnormals Compute normals of a triangular mesh
bone1 predefined colors for bone and skin
bone2 predefined colors for bone and skin
bone3 predefined colors for bone and skin
cExtract extract information about fixed landmarks, curves and patches from and atlas generated by "landmark"
closemeshKD Project coordinates onto a target triangular surface mesh.
conv2backf invert faces' orientation of triangular mesh
covW calculate the pooled within groups covariance matrix
crossp calculate the orthogonal complement of a 3D-vector
CVA Canonical Variate Analysis
deformGrid3d visualise differences between two superimposed sets of 3D landmarks
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 a prediction model
exVar.lm calculate variance of a distribution stemming from a prediction model
exVar.mvr calculate variance of a distribution stemming from a prediction model
file2mesh Import 3D surface mesh files
find.outliers Graphical interface to find outliers and/or to switch mislabeld landmarks
fixLMtps estimate missing landmarks
groupPCA Perform PCA based of the group means' covariance matrix
histGroup plot histogram for multiple groups.
lineplot plot lines between landmarks
mesh2grey convert a colored mesh to greyscale.
mesh2mesh projects the vertices of a mesh onto the surface of another one.
mesh2obj export mesh objects to disk.
mesh2ply export mesh objects to disk.
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.
Morpho loads of stuff relating to Geometric Morphometrics and shape analysis
name2factor extract data from array names
name2num extract data from array names
obj2mesh Import 3D surface mesh files
pcaplot3d visualization of shape change
pcaplot3d.nosymproc visualization of shape change
pcaplot3d.symproc visualization of shape change
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.
plotNormals plots the normals of a triangular surface mesh.
ply2mesh Import 3D surface mesh files
proc.weight calculate weights inverse to the distances from the specified observation.
procSym Procrustes registration
projRead Project points onto the closest point on a mesh
qqmat Q-Q plot to assess normality of data
ray2mesh projects the vertices of a mesh onto the surface of another one.
read.csv.folder batch import data from files
read.lmdta read dta files
read.mpp Read saved pick-points from meshlab
read.pts reads pts files
readallTPS Import landmarks and outlines from TPS files
regdist correlation between shape space and tangent space
regdist.raw correlation between shape space and tangent space
relaxLM relax one specific 3D 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
rmUnrefVertex some little helpers for vertex operations on triangular meshes
rmVertex some little helpers for vertex operations on triangular meshes
rotaxis3d Rotate an object around an arbitrary axis in 3D
rotaxis3d.matrix Rotate an object around an arbitrary axis in 3D
rotaxis3d.mesh3d Rotate an object 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
scalemesh scale a mesh of class "mesh3d"
showPC convert PCs to landmark configuration
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
slider3d slides Semilandmarks along curves and surfaces in 3D by minimising bending energy of a thin-plate spline deformation.
tanplan calculate the orthogonal complement of a 3D-vector
tps3d thin plate spline mapping
typprob calculate typicality probabilities
typprobClass calculate typicality probabilities
unrefVertex some little helpers for vertex operations on triangular meshes
vecx convert an 3D array into a matrix
vert2points some little helpers for vertex operations on triangular meshes
warp.mesh warping a mesh onto another configuration
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.pts exports a matrix containing landmarks into .pts format