Description Usage Details Value Available Methods Note See Also

`mc3_mthds`

returns a list of normalization methods to be used
during level 3 multiple-concentration processing.

1 |

The functions contained in the list returned by `mc3_mthds`

take
'aeids' (a numeric vector of aeid values) and returns a list of expressions
to be executed in the `mc3`

(not exported) function environment. The
functions are described here for reference purposes, The
`mc3_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.

A list of functions

The methods are broken into three types, based on what fields they define. Different methods are used to define "bval" (the baseline value), "pval" (the positive control value), and "resp" (the final response value).

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

More information about the level 3 multiple-concentration processing is available in the package vignette, "Pipeline_Overview."

- bval.apid.nwlls.med
Calculate bval as the median of cval for wells with wllt equal to "n," by apid.

- bval.apid.lowconc.med
Calculate bval as the median of cval for wells with wllt equal to "t" and cndx equal to 1 or 2, by apid.

- bval.apid.twlls.med
Calculate bval as the median of cval for wells with wllt equal to "t," by apid.

- bval.apid.tn.med
Calculate bval as the median of cval for wells with wllt equal to "t" or "n," by apid.

- bval.apid.nwllslowconc.med
Calculate bval as the median of cval for wells with wllt equal to "n" or wells with wllt equal to "t" and cndx equal to 1 or 2, by apid.

- bval.spid.lowconc.med
Calculate bval as the median of cval for wells with wllt equal to "t" and cndx equal to 1, 2, or 3, by spid.

- bval.apid.nwllstcwllslowconc.med
Calculate bval as the median of cval for wells with wllt equal to "n" or cndx equal to 1 or 2 and wllt equal to "t" or "c" by apid.

- pval.apid.pwlls.med
Calculate pval as the median of cval for wells with wllt equal to "p," by apid.

- pval.apid.mwlls.med
Calculate pval as the median of cval for wells with wllt equal to "m," by apid.

- pval.apid.medpcbyconc.max
First calculate the median of cval for wells with wllt equal to "p" or "c," by wllt, conc, and apid. Then calculate pval as the maximum of the calculated medians, by apid.

- pval.apid.medpcbyconc.min
First calculate the median of cval for wells with wllt equal to "p" or "c," by wllt, conc, and apid. Then calculate pval as the minimum of the calculated medians, by apid.

- pval.apid.medncbyconc.min
First calculate the median of cval for wells with wllt equal to "m" or "o," by wllt, conc, and apid. Then calculate pval as the minimum of the calculated medians, by apid.

- pval.apid.pmv.min
First calculate the median of cval for wells with wllt equal to "p," "m," or "v," by wllt, conc, and apid. Then calculate pval as the minimum of the calculated medians, by apid.

- pval.apid.pmv.max
First calculate the median of cval for wells with wllt equal to "p," "m," or "v," by wllt, conc, and apid. Then calculate pval as the maximum of the calculated medians, by apid.

- pval.apid.f.max
First calculate the median of cval for wells with wllt equal to "f," by wllt, conc, and apid. Then calculate pval as the maximum of the calculated medians, by apid.

- pval.apid.f.min
First calculate the median of cval for wells with wllt equal to "f," by wllt, conc, and apid. Then calculate pval as the minimum of the calculated medians, by apid.

- pval.apid.p.max
First calculate the median of cval for wells with wllt equal to "p," by wllt, conc, and apid. Then calculate pval as the maximum of the calculated medians, by apid.

- pval.apid.p.min
First calculate the median of cval for wells with wllt equal to "p," by wllt, conc, and apid. Then calculate pval as the minimum of the calculated medians, by apid.

- pval.apid.v.min
First calculate the median of cval for wells with wllt equal to "v," by wllt, conc, and apid. Then calculate pval as the minimum of the calculated medians, by apid.

- pval.zero
Define pval as 0.

- resp.pc
Calculate resp as

*(cval - bval)/(pval - bval)*100*.- resp.pc.pval.cor
Calculate resp as

*(cval - bval)/(pval)*100*.- resp.fc
Calculate resp as

*cval/bval*.- resp.logfc
Calculate resp as

*cval - bval*.- resp.log2
Take the logarithm of resp with base 2.

- resp.mult25
Multiply resp by 25.

- resp.scale.mad.log2fc
Multiply resp by the scale factor

*log2(1.2)/(3*bmad)*.- resp.scale.quant.log2fc
Determine the maximum response

*md*where*md*= abs(1st centile - 50th centile) or abs(99th centile - 50th centile), whichever is greater. Scale the response such that 20 percent of md equals*log2(1.2)*.- resp.multneg1
Multiply resp by -1.

- resp.shiftneg.3bmad
Shift all resp values less than -3*bmad to 0.

- resp.shiftneg.6bmad
Shift all resp values less than -6*bmad to 0.

- resp.shiftneg.10bmad
Shift all resp values less than -10*bmad to 0.

- resp.blineshift.3bmad.repi
Shift resp values with the blineShift function by repi, where the window (wndw) is 3*bmad.

- resp.blineshift.50.repi
Shift resp values with the blineShift function by repi, where the window (wndw) is 50.

- resp.blineshift.3bmad.spid
Shift resp values with the blineShift function by spid, where the window (wndw) is 3*bmad.

- resp.blineshift.50.spid
Shift resp values with the blineShift function by spid, where the window (wndw) is 50.

- none
Do no normalization; make resp equal to cval.

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

`mc3`

, `Method functions`

to query what
methods get applied to each aeid

USEPA/CompTox-ToxCast-tcpl documentation built on May 5, 2019, 4:48 p.m.

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