molaR_Batch: Run a batch of molaR analyses

Description Usage Arguments Details

View source: R/molaR_Batch.R

Description

A function which automates molaR analyses. User simply sets up the functions they want run and can leave the computer to do the rest.

Usage

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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 = 5.625, 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.

Details

This function allows a user to set the analyses from molaR they want to run, along with the specific parameters for each function and have a whole batch of PLY files analyzed and saved to a csv file. Function will perform analyses on all PLY files in the working directory or user can specify a pathname to a folder containing PLY files. Output saves to the folder that contains the analyzed PLY files.

This function will accept a vector of parameters for any of the function arguments if the user wishes to vary the settings over the course of the batch run. It is recommended that when making use of this feature the Parameters argument is set to TRUE for a record of how analyses were performed.

Note that batch processing updates will not display by default if using RGui for Windows. Be sure to disable Misc -> Buffered output (Ctrl+W) if you wish to view batch processing progress in RGui for Windows.


molaR documentation built on Sept. 20, 2017, 5:07 p.m.