# Dental Surface Complexity Measurement Tools

## Documentation for package ‘molaR’ version 4.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

Check2D | Plot 2D footprint and footprint triangle points to check for erros in 2D calculation
clustered_patches | A clustering function
compute_energy_per_face | Function will compute the DNE per face.
cross | Cross product function
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 DNE calculation.
face_areas | Function to calculate face areas.
Face_Normals | Function to find Face Normals
Hills | Hills - sine-cosine plane
Hills.mesh | Hills - sine-cosine plane
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
OPCr | Calculate average orientation patch count after several rotations
OPCr_Example1 | OPCr_Example1 - object created by OPCr function used as an example.
OPCr_Example1.list | OPCr_Example1 - object created by OPCr function used as an example.
OPCr_Example2 | OPCr_Example2 - object created by OPCr function used as an example.
OPCr_Example2.list | OPCr_Example2 - object created by OPCr function used as an example.
OPC_Legend | function for building a legend in OPC plots
patches_for_each_direction | Function for gathering the patches for each direction
patches_per | A function for patches within each face
patch_details | Function for gathering patch details for each Orientation patch
plyClip | Clip a ply file
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
repmat | Replicate a matrix
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
Tooth | Tooth - scan of USNM_112176 lower M1 from Chlorocebus spp.
Tooth.mesh | Tooth - scan of USNM_112176 lower M1 from Chlorocebus spp.
tr | Trace function
vertex_to_face_list | function for making a list of faces on each vertex