R/mthd_funcs.R

In tcpl: ToxCast Data Analysis Pipeline

#' @name Method functions
#' @rdname mthd_funcs
#' @title Functions for managing processing methods
#'
#' @description
#' These functions are used to manage which methods are used to process data.
#' They include methods for assigning, clearing, and loading the assigned 
#' methods. Also, \code{tcplMthdList} lists the available methods. 
#' 
#' @param lvl Integer of length 1, the method level
#' @param id Integer, the assay component or assay endpoint id(s)
#' @param mthd_id Integer, the method id(s)
#' @param ordr Integer, the order in which to execute the analysis methods,
#' must be the same length as mthd_id, does not apply to levels 5 or 6
#' @param type Character of length 1, the data type, "sc" or "mc"
#' 
#' @details
#' \code{tcplMthdLoad} loads the assigned methods for the given level and 
#' ID(s). Similarly, \code{tcplMthdList} displays the available methods for 
#' the given level. These two functions do not make any changes to the 
#' database.
#' 
#' Unlike the \code{-Load} and \code{-List} functions, the \code{-Assign} and 
#' \code{-Clear} functions alter the database and trigger a delete cascade. 
#' \code{tcplMthdAssign} assigns methods to the given ID(s), and 
#' \code{tcplMthdClear} removes methods. In addition to the method ID 
#' ('mthd_id'), assigning methods at some levels require an order ('ordr'). 
#' The 'ordr' parameter is necessary to allow progression of methods at level
#' one for single-concentration processing, and levels two and three for 
#' multiple-concentration processing. More information about method assignments 
#' and the delete cascade are available in the package vignette. 
#' 
#' @examples 
#' ## Store the current config settings, so they can be reloaded at the end 
#' ## of the examples
#' conf_store <- tcplConfList()
#' tcplConfDefault()
#' 
#' ## tcplListMthd allows the user to display the available methods for 
#' ## a given level and data type
#' head(tcplMthdList(lvl = 2, type = "mc"))
#' 
#' ## tcplLoadMthd shows which methods are assigned for the given ID, level,
#' ## and data type. Here we will show how to register, load, and clear methods
#' ## using an acid not in the example database. Note: There is no check for
#' ## whether an ID exists before assigning/clearing methods. 
#' tcplMthdLoad(lvl = 2, id = 55, type = "mc")
#' 
#' \dontrun{
#' ## ACID 55 does not have any methods. Assign methods from the list above. 
#' tcplMthdAssign(lvl = 2, 
#'                id = 55, 
#'                mthd_id = c(3, 4, 2), 
#'                ordr = 1:3, 
#'                type = "mc")
#' ## Method assignment can be done for multiple assays, too. 
#' tcplMthdAssign(lvl = 2, 
#'                id = 53:54, 
#'                mthd_id = c(3, 4, 2), 
#'                ordr = 1:3, 
#'                type = "mc")
#'                
#' ## Cleanup example method assigments
#' tcplMthdClear(lvl = 2, id = 53:55, type = "mc")
#' }
#' ## Reset configuration
#' options(conf_store)
NULL