Usage
molaR_Batch(pathname = getwd(), filename = "molaR_Batch.csv", DNE = TRUE, RFI = TRUE, OPCr = TRUE, OPC = FALSE, Slope = TRUE, Details = FALSE, DNE_outliers = 0.1, DNE_BoundaryDiscard = "Leg", RFI_alpha = 0.01, OPCr_steps = 8, OPCr_stepSize = 5.626, OPCr_minimum_faces = 3, OPCr_minimum_area = 0, OPC_rotation = 0, OPC_minimum_faces = 3, OPC_minimum_area = 0, Slope_Guess = FALSE, Parameters = FALSE)
Arguments
pathname
The path to the file containing all the PLY surfaces to be
analyzed. Defaults to the working directory
filename
Name for the output csv file.
DNE
logical indicating whether or not to perform DNE calculation Defaults
to true
RFI
logical indicating whether or not to perform RFI calculation Defaults to
true
OPCr
logical indicating whether or not to perform OPCr calculation
Defaults to true
OPC
logical indicating whether or not to perform OPC calculation Defaults
to false
Slope
logical indicating whether or not to perform Slope calculation, Defaults
to true
Details
logical indicating whether or not to save the details of the RFI and
OPCr calculations
DNE_outliers
the percentile at which outliers will be excluded is passed to
the DNE function, defaults to 0.1
DNE_BoundaryDiscard
is a logical indicating how
to handle the exclusion of the faces on the edge of the surface, defaults to excluding
faces which have a leg on the boundary.
RFI_alpha
the size of the alpha passed to RFI
function, defaults to 0.01
OPCr_steps
the number of steps the OPCr function should take, is passed to
the OPCr function. Defaults to 8
OPCr_stepSize
the size of each rotation. Passed to the OPCr function.
Defaults to 5.626 degrees
OPCr_minimum_faces
sets the lower boundary for number of faces a patch
must have for inclusion in total count. Defaults to 3 or more.
OPCr_minimum_area
sets the lower boundary for percentage of the surface
area a patch must make up for inclusion in the total patch count. Cannot be used with
minimum_faces on. Defaults to zero
OPC_rotation
amount of rotation to apply during OPC calculation. Defaults
to zero
OPC_minimum_faces
minimum number of faces a patch must contain to be
counted in the OPC function. Defaults to 3.
OPC_minimum_area
minimum percentage of the surface area a patch must
make up to be counted in the OPC function. Defaults to off
Slope_Guess
logical indicating whether or not to Guess as to the orientation
of the surface during the Slope calculation (see Slope function for details)
Parameters
defaults to off. When engaged a list of all the parameters used
during molaR analysis will be appended to the output file.