MC4_Methods: List of level 4 multiple-concentration methods for...

In tcpl: ToxCast Data Analysis Pipeline

List of level 4 multiple-concentration methods for calculating bmad

Description

mc4_mthds returns a list of methods to be used during level 4 multiple-concentration processing for calculating bmad

Usage

mc4_mthds()

Details

The functions contained in the list returned by mc4_mthds take aeids (a numeric vector of aeid values) and returns a list of expressions to be executed in the mc4 (not exported) function environment. The functions are described here for reference purposes, The mc4_mthds function is not exported, nor is it intended for use.

All available methods are described in the Available Methods section, listed by the type of function and the function/method name.

Value

A list of functions

Available Methods

Although it does not say so specifically in each description, all methods are applied by aeid.

More information about the level 4 multiple-concentration processing is available in the package vignette, "Data_processing."

bmad.aeid.lowconc.twells

Calculate the baseline median absolute value (bmad) as the median absolute deviation of normalized response values (rep) for test compound wells (wllt = t) with concentration index (cndx) equal to 1 or 2. Calculate one standard deviation of the normalized response for test compound wells (wllt = t) with a concentration index (cndx) of 1 or 2; onesd = sqrt(sum((resp - mean resp)^2)/sample size - 1). Onesd is used to establish BMR and therefore required for tcplfit2 processing.

bmad.aeid.lowconc.nwells

Calculate the baseline median absolute value (bmad) as the median absolute deviation of normalized response values (resp) for neutral control wells (wllt = n). Calculate one standard deviation of the normalized response for neutral control wells (wllt = n); onesd = sqrt(sum((resp - mean resp)^2)/sample size - 1). Onesd is used to establish BMR and therefore required for tcplfit2 processing.

bidirectional.false

Limits bidirectional fitting and processes data in positive analysis direction only. Use for gain-of-signal or inverted data.

bmad5.onesd16.static

Replace baseline median absolute deviation (bmad) with 5 and one standard deviation (osd) of the normalized response for test compound wells (wllt = t) with a concentration index (cndx) of 1 or 2 with 16. Typically used for binary data where values would otherwise be 0; non-zero values are required for tcplfit2 processing.

no.unbounded.models

Exclude unbounded models and only fit data to bounded models (hill, gnls, exp4 and exp5).

Note

This function is not exported and is not intended to be used by the user.

See Also

mc4, Method functions to query what methods get applied to each aeid

tcpl documentation built on Oct. 10, 2024, 1:07 a.m.