Documentation of outputs

[john-harrold]

I may have missed this in the documentation. If so, just point me to it. But is there some detailed documentation of the various outputs? Like what they exactly mean and how they are calculated? I find some of them to be a little ambiguous: half.life vs thalf.eff.obs vs thalf.eff.pred.

[billdenney]

The parameters are generally described in the help page to the equivalent function (the link isn't well documented). You can see what function is used for each calculation by looking at the output of get.interval.cols(). And, that also includes a brief description of the parameter.

For example, to see half.life:

> get.interval.cols()$half.life
$FUN
[1] "pk.calc.half.life"

$values
[1] FALSE  TRUE

$desc
[1] "The (terminal) half-life"

$formalsmap
list()

$depends
[1] "tmax"  "tlast"

$datatype
[1] "interval"

>

The "desc" is a description of the parameter, and "FUN" is the name of the function that calculates it. (For the purposes of this, you can ignore the other parts of this output.)

I'm going to leave this issue open so that I continue improving the documentation of the calculations.

[billdenney]

@john-harrold I just pushed some extensive documentation updates. If you have future questions about documentation, please don't hesitate to ask!

[john-harrold]

Hello Bill. Sorry to resurrect this, but I'm writing some documentation on functions that depend on PKNCA output. Can you point me to which function documents the outputs? Specifically how the different outputs are calculated?

[billdenney]

@john-harrold, I'm uncertain of what you're looking for here. The parameters are defined by name, and the calculations are the same as standard calculations (for which any textbook provides the equations). If you're wanting to see the equations themselves, you can see it by reviewing the code. For example, to see thalf.eff, you can just type pk.calc.thalf.eff at the R console after loading PKNCA and see the equation:

> pk.calc.thalf.eff
function(mrt)
  log(2)*mrt
<environment: namespace:PKNCA>
>

[john-harrold]

Sure. For example what is the difference between the obs and pred variants on AUCinf? For example how are aucinf.obs and aucinf.pred different? Sorry if I'm being dense here.

…

On Fri, Jul 12, 2019 at 9:16 AM Bill Denney ***@***.***> wrote: @john-harrold <https://github.com/john-harrold>, I'm uncertain of what you're looking for here. The parameters are defined by name, and the calculations are the same as standard calculations (for which any textbook provides the equations). If you're wanting to see the equations themselves, you can see it by reviewing the code. For example, to see thalf.eff, you can just type pk.calc.thalf.eff at the R console after loading PKNCA and see the equation: > pk.calc.thalf.efffunction(mrt) log(2)*mrt<environment: namespace:PKNCA>> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#81?email_source=notifications&email_token=AAYF5VBFF7K7M62TZ6YCFKLP7CU4PA5CNFSM4FSJRFH2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZ2GUHA#issuecomment-510945820>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAYF5VFAPPBQJUDCKCKMCPTP7CU4PANCNFSM4FSJRFHQ> .

-- John :wq

[billdenney]

Documenting everything will take some time. Until I’m able to do so, you can use the PhUSE paper to help: https://www.phusewiki.org/wiki/images/e/ed/PhUSE_CSS_WhitePaper_PK_final_25March2014.pdf

[billdenney]

I think that this is now documented in http://billdenney.github.io/pknca/articles/Selection-of-Calculation-Intervals.html#parameters-available-for-calculation-in-an-interval-1

If this doesn't cover what you're looking for, please reopen the issue.

[john-harrold]

This is perfect. Thankyou!