molaR: Dental Surface Complexity Measurement Tools
Version 4.2

Surface topography calculations of Dirichlet's normal energy, relief index, surface slope, and orientation patch count for teeth using scans of enamel caps. Importantly, for the relief index and orientation patch count calculations to work, the scanned tooth files must be oriented with the occlusal plane parallel to the x and y axes, and perpendicular to the z axis. The files should also be simplified, and smoothed in some other software prior to uploading into R.

AuthorJames D. Pampush [aut, cre, cph], Julia M. Winchester [aut, cph], Paul E. Morse [aut, cph], Alexander Q. Vining [aut, cph]
Date of publication2016-08-31 01:26:14
MaintainerJames D. Pampush <jdpampush@gmail.com>
LicenseACM
Version4.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("molaR")

Popular man pages

DNE: Calculate Dirichlet normal energy of a surface
DNE_Legend: Make legend for DNE3d plot
OPCr: Calculate average orientation patch count after several...
read.AVIZO.ply: Read mesh data from ply files saved by AVIZO
RFI: Calculate Boyer's (2008) relief index for a surface
RFI3d: Plot 3D and 2D areas of a mesh used to calculate relief index
Slope: Function to calculate the average slope of a surface
See all...

All man pages Function index File listing

Man pages

clustered_patches: A clustering function
compute_energy_per_face: Function will compute the DNE per face.
cSize: Centroid Size Function
Directional_Bins: This bins the faces into directional categories
DNE: Calculate Dirichlet normal energy of a surface
DNE3d: Plot results of a DNE analysis of a surface
DNE_Legend: Make legend for DNE3d plot
edge_vertices: Function for finding the edge vertices
Equal_Vertex_Normals: Important function for re-doing the vertex normals for the...
ex_tooth1: 4149_DU-LP-09_LM1
ex_tooth2: 4147_DU-LP-07_LM1
face_areas: Function to calculate face areas.
Face_Normals: Function to find Face Normals
index_paired_directed_faces: Index of paired faces with directions
molaR_Batch: Run a batch of molaR analyses
molaR_bgplot: Internal function for making molaR plot legends
molaR_Clean: Clean up problem ply files
OPC: Calculate orientation patch count of a surface
OPC3d: Plot results of OPC analysis of a surface
OPC_Legend: function for building a legend in OPC plots
OPCr: Calculate average orientation patch count after several...
patch_details: Function for gathering patch details for each Orientation...
patches_for_each_direction: Function for gathering the patches for each direction
patches_per: A function for patches within each face
plyZClip: Function which will clip a plyFile
read.AVIZO.ply: Read mesh data from ply files saved by AVIZO
remove_boundary_faces: Remove boundary faces
remove_outliers: Mask outliers on some faces
RFI: Calculate Boyer's (2008) relief index for a surface
RFI3d: Plot 3D and 2D areas of a mesh used to calculate relief index
RFI_Legend: function for building a legend for RFI
Slope: Function to calculate the average slope of a surface
Slope3d: Plot results of a Slope analysis of a surface
Slope_Legend: Plotting subfunction for making slope plot legend
tr: Trace function
vertex_to_face_list: function for making a list of faces on each vertex

Functions

DNE Man page Source code
DNE3d Man page Source code
DNE_Legend Man page Source code
Directional_Bins Man page Source code
Equal_Vertex_Normals Man page Source code
Face_Normals Man page Source code
OPC Man page Source code
OPC3d Man page Source code
OPC_Legend Man page Source code
OPCr Man page Source code
RFI Man page Source code
RFI3d Man page Source code
RFI_Legend Man page Source code
Slope Man page Source code
Slope3d Man page Source code
Slope_Legend Man page Source code
cSize Man page Source code
clump Source code
clustered_patches Man page Source code
compute_energy_per_face Man page Source code
edge_vertices Man page Source code
ex_tooth1 Man page
ex_tooth2 Man page
face_areas Man page Source code
getClusters Source code
index_paired_directed_faces Man page Source code
molaR_Batch Man page Source code
molaR_Clean Man page Source code
molaR_bgplot Man page Source code
patch_details Man page Source code
patches_for_each_direction Man page Source code
patches_per Man page Source code
plyZClip Man page Source code
read.AVIZO.ply Man page Source code
remove_boundary_faces Man page Source code
remove_outliers Man page Source code
tr Man page Source code
vertex_to_face_list Man page Source code

Files

inst
inst/doc
inst/doc/molaR_vignette.html
inst/doc/molaR_vignette.R
inst/doc/molaR_vignette.Rmd
NAMESPACE
data
data/ex_tooth2.RData
data/ex_tooth1.RData
R
R/read.AVIZO.ply.R
R/Directional_Bins.R
R/edge_vertices.R
R/molaR_Clean.R
R/RFI3d.R
R/remove_outliers.R
R/molaR_bgplot.R
R/OPC_Legend.R
R/compute_energy_per_face.R
R/molaR_Batch.R
R/OPCr.R
R/DNE.R
R/OPC3d.R
R/patch_details.R
R/DNE_Legend.R
R/Face_Normals.R
R/OPC.R
R/remove_boundary_faces.R
R/vertex_to_face_list.R
R/index_paired_directed_faces.R
R/Slope_Legend.R
R/cSize.R
R/patches_for_each_direction.R
R/RFI_Legend.R
R/patches_per.R
R/clustered_patches.R
R/face_areas.R
R/tr.R
R/RFI.R
R/Equal_Vertex_Normals.R
R/Slope3d.R
R/DNE3d.R
R/Slope.R
R/plyZClip.R
vignettes
vignettes/molaR_vignette.Rmd
MD5
build
build/vignette.rds
build/molaR.pdf
DESCRIPTION
man
man/OPCr.Rd
man/molaR_Clean.Rd
man/DNE_Legend.Rd
man/OPC3d.Rd
man/ex_tooth1.Rd
man/vertex_to_face_list.Rd
man/RFI_Legend.Rd
man/Face_Normals.Rd
man/RFI.Rd
man/plyZClip.Rd
man/Directional_Bins.Rd
man/DNE3d.Rd
man/molaR_Batch.Rd
man/edge_vertices.Rd
man/cSize.Rd
man/molaR_bgplot.Rd
man/Slope_Legend.Rd
man/compute_energy_per_face.Rd
man/patches_for_each_direction.Rd
man/ex_tooth2.Rd
man/read.AVIZO.ply.Rd
man/Equal_Vertex_Normals.Rd
man/Slope3d.Rd
man/clustered_patches.Rd
man/remove_boundary_faces.Rd
man/index_paired_directed_faces.Rd
man/OPC.Rd
man/OPC_Legend.Rd
man/face_areas.Rd
man/remove_outliers.Rd
man/DNE.Rd
man/tr.Rd
man/Slope.Rd
man/patches_per.Rd
man/patch_details.Rd
man/RFI3d.Rd
molaR documentation built on May 19, 2017, 2:01 p.m.

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