molaR (version 4.5)

OPC: Calculate orientation patch count of a surface

Description

A function that bins patches of a mesh surface that share general orientation and sums the number of unique patches given certain parameters Modified into 3D from the original 2.5D method described by Evans et al. (2007) High-level similarity of dentitions in carnivorans and rodents.Nature 445:78-81 doi: 10.1038 nature05433

Usage

OPC(plyFile, rotation = 0, minimum_faces = 3, minimum_area = 0)

Arguments

plyFile

An object of classes "mesh3d" and "shape3d" with calculated normals

rotation

Rotates the file in degrees about the center vertical axis

minimum_faces

Minimum number of ply faces required for a patch to be counted towards the total patch count

minimum_area

Minimum proportion (100 patch must occupy to be counted towards the total patch count

Details

The function requires a mesh object created by reading in a ply file utilizing either the read.ply, vcgPlyread, or read.AVIZO.ply function

Orientation patch count is calculated on meshes that represent specimen surfaces and have already been downsampled to 10,000 faces and pre-smoothed in a 3D data editing program. Alignment of the point cloud will have a large effect on patch orientation and must be done in a 3D data editing program such as Avizo, or using the R package auto3dgm prior to creating and reading in the ply file. The occlusal surface of the specimen must be made parallel to the X- and Y-axes and perpendicular to the Z-axis.

The default for minimum_faces is to ignore patches consisting of only a single face on the mesh. Changing the minimum_area value will disable minimum_faces.

Examples

# NOT RUN {
OPC_output <- OPC(Tooth)
summary(OPC_output)
# }