Check2D                 Plot 2D footprint and footprint triangle points
                        to check for erros in 2D calculation
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
Directional_Bins        This bins the faces into directional categories
Equal_Vertex_Normals    Important function for re-doing the vertex
                        normals for the DNE calculation.
Face_Normals            Function to find Face Normals
Hills                   Hills - sine-cosine plane
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 rotations
OPCr_Example1           OPCr_Example1 - object created by OPCr function
                        used as an example.
OPCr_Example2           OPCr_Example2 - object created by OPCr function
                        used as an example.
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.
cSize                   Centroid Size Function
clustered_patches       A clustering function
compute_energy_per_face
                        Function will compute the DNE per face.
cross                   Cross product function
edge_vertices           Function for finding the edge vertices
face_areas              Function to calculate face areas.
index_paired_directed_faces
                        Index of paired faces with directions
molaR_Batch             Run a batch of molaR analyses
molaR_Clean             Clean up problem ply files
molaR_bgplot            Internal function for making molaR plot legends
patch_details           Function for gathering patch details for each
                        Orientation patch
patches_for_each_direction
                        Function for gathering the patches for each
                        direction
patches_per             A function for patches within each face
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
tr                      Trace function
vertex_to_face_list     function for making a list of faces on each
                        vertex
