From 4a918da6d5f971335b74b0fc83cb08f5c3163f95 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 21 Jul 2017 14:42:14 +0200 Subject: Rename twa to max_twa_parent, update docs --- vignettes/twa.Rmd | 21 +++++++++++++++------ vignettes/twa.html | 19 ++++++++++--------- 2 files changed, 25 insertions(+), 15 deletions(-) (limited to 'vignettes') diff --git a/vignettes/twa.Rmd b/vignettes/twa.Rmd index 60188223..c4fe861f 100644 --- a/vignettes/twa.Rmd +++ b/vignettes/twa.Rmd @@ -11,10 +11,14 @@ vignette: > Since version 0.9.45.1 of the 'mkin' package, a function for calculating time weighted average concentrations for decline kinetics (*i.e.* only -for the compound applied in the experiment) is included. +for the compound applied in the experiment) is included. Strictly +speaking, they are maximum moving window time weighted average concentrations, +*i.e.* the maximum time weighted average concentration that can be found +when moving a time window of a specified width over the decline curve. -Time weighted average concentrations for the DFOP model are calculated using -the formulas given in the FOCUS kinetics guidance [@FOCUSkinetics2014, p. 251]: +Time weighted average concentrations for the SFO, FOMC and the DFOMP model are +calculated using the formulas given in the FOCUS kinetics guidance +[@FOCUSkinetics2014, p. 251]: SFO: @@ -22,7 +26,7 @@ $$c_\textrm{twa} = c_0 \frac{\left( 1 - e^{- k t} \right)}{ k t} $$ FOMC: -$$c_\textrm{twa} = c_0 \frac{\beta}{t (1 - \alpha)} +$$c_\textrm{twa} = c_0 \frac{\beta}{t (1 - \alpha)} \left( \left(\frac{t}{\beta} + 1 \right)^{1 - \alpha} - 1 \right) $$ DFOP: @@ -32,7 +36,7 @@ $$c_\textrm{twa} = \frac{c_0}{t} \left( \frac{1-g}{k_2} \left( 1 - e^{- k_2 t} \right) \right) $$ Often, the ratio between the time weighted average concentration $c_\textrm{twa}$ -and the initial concentration $c_0$ +and the initial concentration $c_0$ $$f_\textrm{twa} = \frac{c_\textrm{twa}}{c_0}$$ @@ -46,7 +50,7 @@ $$f_\textrm{twa} = \frac{\left( 1 - e^{- k t} \right)}{k t} $$ FOMC: -$$f_\textrm{twa} = \frac{\beta}{t (1 - \alpha)} +$$f_\textrm{twa} = \frac{\beta}{t (1 - \alpha)} \left( \left(\frac{t}{\beta} + 1 \right)^{1 - \alpha} - 1 \right) $$ DFOP: @@ -55,3 +59,8 @@ $$f_\textrm{twa} = \frac{1}{t} \left( \frac{g}{k_1} \left( 1 - e^{- k_1 t} \right) + \frac{1-g}{k_2} \left( 1 - e^{- k_2 t} \right) \right) $$ +Note that a method for calculating maximum moving window time weighted average +concentrations for any model fitted by 'mkinfit', and also for metabolites in +such models, can be found in the 'pfm' package, which is currently not published on +CRAN, but available from [github](https://github.com/jranke/pfm) and +[documented](https://pkgdown.jrwb.de/pfm) at my website. diff --git a/vignettes/twa.html b/vignettes/twa.html index 6861d9fc..f885cb8a 100644 --- a/vignettes/twa.html +++ b/vignettes/twa.html @@ -4,14 +4,14 @@ - + - + Calculation of time weighted average concentrations with mkin @@ -21,7 +21,7 @@ - + @@ -119,17 +119,17 @@ $(document).ready(function () {

Calculation of time weighted average concentrations with mkin

Johannes Ranke

-

2017-03-28

+

2017-07-21

-

Since version 0.9.45.1 of the ‘mkin’ package, a function for calculating time weighted average concentrations for decline kinetics (i.e. only for the compound applied in the experiment) is included.

-

Time weighted average concentrations for the DFOP model are calculated using the formulas given in the FOCUS kinetics guidance (FOCUS Work Group on Degradation Kinetics 2014, 251):

+

Since version 0.9.45.1 of the ‘mkin’ package, a function for calculating time weighted average concentrations for decline kinetics (i.e. only for the compound applied in the experiment) is included. Strictly speaking, they are maximum moving window time weighted average concentrations, i.e. the maximum time weighted average concentration that can be found when moving a time window of a specified width over the decline curve.

+

Time weighted average concentrations for the SFO, FOMC and the DFOMP model are calculated using the formulas given in the FOCUS kinetics guidance (FOCUS Work Group on Degradation Kinetics 2014, 251):

SFO:

\[c_\textrm{twa} = c_0 \frac{\left( 1 - e^{- k t} \right)}{ k t} \]

FOMC:

-

\[c_\textrm{twa} = c_0 \frac{\beta}{t (1 - \alpha)} +

\[c_\textrm{twa} = c_0 \frac{\beta}{t (1 - \alpha)} \left( \left(\frac{t}{\beta} + 1 \right)^{1 - \alpha} - 1 \right) \]

DFOP:

\[c_\textrm{twa} = \frac{c_0}{t} \left( @@ -141,12 +141,13 @@ $(document).ready(function () {

SFO:

\[f_\textrm{twa} = \frac{\left( 1 - e^{- k t} \right)}{k t} \]

FOMC:

-

\[f_\textrm{twa} = \frac{\beta}{t (1 - \alpha)} +

\[f_\textrm{twa} = \frac{\beta}{t (1 - \alpha)} \left( \left(\frac{t}{\beta} + 1 \right)^{1 - \alpha} - 1 \right) \]

DFOP:

\[f_\textrm{twa} = \frac{1}{t} \left( \frac{g}{k_1} \left( 1 - e^{- k_1 t} \right) + \frac{1-g}{k_2} \left( 1 - e^{- k_2 t} \right) \right) \]

+

Note that a method for calculating maximum moving window time weighted average concentrations for any model fitted by ‘mkinfit’, and also for metabolites in such models, can be found in the ‘pfm’ package, which is currently not published on CRAN, but available from github and documented at my website.

FOCUS Work Group on Degradation Kinetics. 2014. Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration. 1.1 ed. http://focus.jrc.ec.europa.eu/dk.

@@ -176,7 +177,7 @@ $(document).ready(function () { (function () { var script = document.createElement("script"); script.type = "text/javascript"; - script.src = "https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"; + script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"; document.getElementsByTagName("head")[0].appendChild(script); })(); -- cgit v1.2.1