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molaR (version 4.5)

Dental Surface Complexity Measurement Tools

Description

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.

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Version

Install

install.packages('molaR')

Monthly Downloads

312

Version

4.5

License

ACM

Maintainer

James D. Pampush

Last Published

March 4th, 2020

Functions in molaR (4.5)

RFI

Calculate Boyer's (2008) relief index for a surface
clustered_patches

A clustering function
molaR_bgplot

Internal function for making molaR plot legends
patch_details

Function for gathering patch details for each Orientation patch
vertex_to_face_list

function for making a list of faces on each vertex
RFI3d

Plot 3D and 2D areas of a mesh used to calculate relief index
compute_energy_per_face

Function will compute the DNE per face.
DNE_Legend

Make legend for DNE3d plot
Slope3d

Plot results of a Slope analysis of a surface
Slope_Legend

Plotting subfunction for making slope plot legend
OPCr_Example1

OPCr_Example1 - object created by OPCr function used as an example.
molaR_Batch

Run a batch of molaR analyses
cSize

Centroid Size Function
plyClip

Clip a ply file
read.AVIZO.ply

Read mesh data from ply files saved by AVIZO
Tooth

Tooth - scan of USNM_112176 lower M1 from Chlorocebus spp.
molaR_Clean

Clean up problem ply files
patches_for_each_direction

Function for gathering the patches for each direction
patches_per

A function for patches within each face
OPCr_Example2

OPCr_Example2 - object created by OPCr function used as an example.
RFI_Legend

function for building a legend for RFI
Slope

Function to calculate the average slope of a surface
OPC_Legend

function for building a legend in OPC plots
remove_outliers

Mask outliers on some faces
edge_vertices

Function for finding the edge vertices
cross

Cross product function
remove_boundary_faces

Remove boundary faces
repmat

Replicate a matrix
face_areas

Function to calculate face areas.
tr

Trace function
OPCr

Calculate average orientation patch count after several rotations
index_paired_directed_faces

Index of paired faces with directions
OPC

Calculate orientation patch count of a surface
OPC3d

Plot results of OPC analysis of a surface
DNE3d

Plot results of a DNE analysis of a surface
Face_Normals

Function to find Face Normals
Hills

Hills - sine-cosine plane
Directional_Bins

This bins the faces into directional categories
Equal_Vertex_Normals

Important function for re-doing the vertex normals for the DNE calculation.
Check2D

Plot 2D footprint and footprint triangle points to check for erros in 2D calculation
DNE

Calculate Dirichlet normal energy of a surface