RFI {molaR}

Calculate relief index for a surface

Description

A function that calculates relief index following Boyer (2008) Relief index of second mandibular molars is a correlate of diet among prosimian primates and other mammals. J Hum Evol 55:1118-1137 doi: 10.1016/j.jhevol.2008.08.002

Usage

RFI(plyFile, alpha = 0.075, findAlpha = FALSE)

Arguments

plyFile

An object of classes 'mesh3d' and 'shape3d'

alpha

Step size for calculating the outline. See details.

findAlpha

Logical indicating that alpha will be auto-calculated. See details.

Details

The function requires an object created by reading in a ply file utilizing either the vcgPlyRead function.

Relief index is calculated by the ratio of three-dimensional surface area to two dimensional area on meshes that represent specimen surfaces and have already been pre-smoothed in a 3D data editing program. Surface alignment will have a large effect on 2D area calculation and must be performed prior to creating and reading in the ply file. The mesh must be oriented such that the occlusal plane is parallel to the X- and Y-axes and perpendicular to the Z-axis (i.e., tooth cusps pointing towards +Z).

The alpha parameter traces the outline of the 2D footprint. An alpha that is too low will result in a tracing error (returning an "Alpha adjustment required" message), while an alpha value that is too high may result in an overestimate of the 2D footprint area by failing to take into account infoldings. The user is encouraged to carefully review results using the RFI3d or Check2D functions.

Alternatively, the findAlpha argument can be used to compute an ideal alpha value for a particular PLY file for use in the RFI calculation. This is defined as the lowest value (to the nearest thousandth) returning no error or warning messages. This feature ensures accuracy, but may increase computing time significantly, depending on the number of alpha values tested. Unfortunately, there is no way to guess an appropriate alpha value a priori. After 100 unsuccessful attempts to find an appropriate alpha, the function will terminate.

The alpha value used in the calculation (whether chosen by the user or auto- computed with findAlpha) is returned in the analysis results.

Examples

RFI_output <- RFI(Tooth, alpha=0.5, findAlpha = FALSE)
summary(RFI_output)