gtoxMthdAssign {GladiaTOX} | R Documentation

## 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, `gtoxMthdList` lists the available methods.

### Usage

    gtoxMthdAssign(lvl, id, mthd_id, ordr = NULL, type)

    gtoxMthdClear(lvl, id, mthd_id = NULL, type)

    gtoxMthdList(lvl, type = "mc")

    gtoxMthdLoad(lvl, id = NULL, type = "mc")

### Arguments

`lvl` | Integer of length 1, the method level
`id` | Integer, the assay component or assay endpoint id(s)
`mthd_id` | Integer, the method id(s)
`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
`type` | Character of length 1, the data type, "sc" or "mc"

### Details

`gtoxMthdLoad` loads the assigned methods for the given level and ID(s). Similarly, `gtoxMthdList` displays the available methods for the given level. These two functions do not make any changes to the database.

Unlike the `-Load` and `-List` functions, the `-Assign` and `-Clear` functions alter the database and trigger a delete cascade. `gtoxMthdAssign` assigns methods to the given ID(s), and `gtoxMthdClear` 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.

### Value

None

### Examples

    ## Not run:
    ## Assign level 2 methods (none for all acid values)
    gtoxMthdAssign(lvl = 2L, id = 1L, mthd_id = 1, ordr = 1, type = "mc")

    ## Process data
    gtoxRun(asid = 1L, slvl = 1, elvl = 6, mc.cores = 2)

    ## End(Not run)

    ## Not run:
    ## Clear level 2 methods
    gtoxMthdClear(lvl = 2L, id = 1L, mthd_id = NULL, type = "mc")

    ## Assign level 2 methods (none for all acid values)
    gtoxMthdAssign(lvl = 2L, id = 1L, mthd_id = 1, ordr = 1, type = "mc")

    ## Process data
    gtoxRun(asid = 1L, slvl = 1, elvl = 6, mc.cores = 2)

    ## End(Not run)

    ## Store the current config settings, so they can be reloaded at the end
    ## of the examples
    conf_store <- gtoxConfList()
    gtoxConfDefault()

    ## gtoxListMthd allows the user to display the available methods for
    ## a given level and data type
    head(gtoxMthdList(lvl = 2, type = "mc"))

    ## gtoxLoadMthd 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.
    gtoxMthdLoad(lvl = 2, id = 1, type = "mc")

    ## Reset configuration
    options(conf_store)

[Package GladiaTOX version 1.0.0 Index]