From 063ae84c199e1223a620fe512ab8713371119f5f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 28 Mar 2017 10:44:50 +0200 Subject: Change vignette format for twa vignette, update docs --- vignettes/twa.Rmd | 57 +++++++++++++++++ vignettes/twa.html | 185 +++++++++++++++++++++++++++++++++++++++++++++++++++++ vignettes/twa.pdf | Bin 146941 -> 0 bytes vignettes/twa.rmd | 57 ----------------- 4 files changed, 242 insertions(+), 57 deletions(-) create mode 100644 vignettes/twa.Rmd create mode 100644 vignettes/twa.html delete mode 100644 vignettes/twa.pdf delete mode 100644 vignettes/twa.rmd (limited to 'vignettes') diff --git a/vignettes/twa.Rmd b/vignettes/twa.Rmd new file mode 100644 index 00000000..60188223 --- /dev/null +++ b/vignettes/twa.Rmd @@ -0,0 +1,57 @@ +--- +title: Calculation of time weighted average concentrations with mkin +author: Johannes Ranke +date: "`r Sys.Date()`" +bibliography: references.bib +vignette: > + %\VignetteEngine{knitr::rmarkdown} + %\VignetteIndexEntry{Calculation of time weighted average concentrations with mkin} + %\VignetteEncoding{UTF-8} +--- + +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 [@FOCUSkinetics2014, p. 251]: + +SFO: + +$$c_\textrm{twa} = c_0 \frac{\left( 1 - e^{- k t} \right)}{ k t} $$ + +FOMC: + +$$c_\textrm{twa} = c_0 \frac{\beta}{t (1 - \alpha)} + \left( \left(\frac{t}{\beta} + 1 \right)^{1 - \alpha} - 1 \right) $$ + +DFOP: + +$$c_\textrm{twa} = \frac{c_0}{t} \left( + \frac{g}{k_1} \left( 1 - e^{- k_1 t} \right) + + \frac{1-g}{k_2} \left( 1 - e^{- k_2 t} \right) \right) $$ + +Often, the ratio between the time weighted average concentration $c_\textrm{twa}$ +and the initial concentration $c_0$ + +$$f_\textrm{twa} = \frac{c_\textrm{twa}}{c_0}$$ + +is needed. This can be calculated from the fitted initial concentration $c_0$ and +the time weighted average concentration $c_\textrm{twa}$, or directly from +the model parameters using the following formulas: + +SFO: + +$$f_\textrm{twa} = \frac{\left( 1 - e^{- k t} \right)}{k t} $$ + +FOMC: + +$$f_\textrm{twa} = \frac{\beta}{t (1 - \alpha)} + \left( \left(\frac{t}{\beta} + 1 \right)^{1 - \alpha} - 1 \right) $$ + +DFOP: + +$$f_\textrm{twa} = \frac{1}{t} \left( + \frac{g}{k_1} \left( 1 - e^{- k_1 t} \right) + + \frac{1-g}{k_2} \left( 1 - e^{- k_2 t} \right) \right) $$ + diff --git a/vignettes/twa.html b/vignettes/twa.html new file mode 100644 index 00000000..6861d9fc --- /dev/null +++ b/vignettes/twa.html @@ -0,0 +1,185 @@ + + + + + + + + + + + + + + + +Calculation of time weighted average concentrations with mkin + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + +

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):

+

SFO:

+

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

+

FOMC:

+

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

+

DFOP:

+

\[c_\textrm{twa} = \frac{c_0}{t} \left( + \frac{g}{k_1} \left( 1 - e^{- k_1 t} \right) + + \frac{1-g}{k_2} \left( 1 - e^{- k_2 t} \right) \right) \]

+

Often, the ratio between the time weighted average concentration \(c_\textrm{twa}\) and the initial concentration \(c_0\)

+

\[f_\textrm{twa} = \frac{c_\textrm{twa}}{c_0}\]

+

is needed. This can be calculated from the fitted initial concentration \(c_0\) and the time weighted average concentration \(c_\textrm{twa}\), or directly from the model parameters using the following formulas:

+

SFO:

+

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

+

FOMC:

+

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

+

DFOP:

+

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

+
+
+

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.

+
+
+ + + + +
+ + + + + + + + diff --git a/vignettes/twa.pdf b/vignettes/twa.pdf deleted file mode 100644 index 879d10c7..00000000 Binary files a/vignettes/twa.pdf and /dev/null differ diff --git a/vignettes/twa.rmd b/vignettes/twa.rmd deleted file mode 100644 index 60188223..00000000 --- a/vignettes/twa.rmd +++ /dev/null @@ -1,57 +0,0 @@ ---- -title: Calculation of time weighted average concentrations with mkin -author: Johannes Ranke -date: "`r Sys.Date()`" -bibliography: references.bib -vignette: > - %\VignetteEngine{knitr::rmarkdown} - %\VignetteIndexEntry{Calculation of time weighted average concentrations with mkin} - %\VignetteEncoding{UTF-8} ---- - -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 [@FOCUSkinetics2014, p. 251]: - -SFO: - -$$c_\textrm{twa} = c_0 \frac{\left( 1 - e^{- k t} \right)}{ k t} $$ - -FOMC: - -$$c_\textrm{twa} = c_0 \frac{\beta}{t (1 - \alpha)} - \left( \left(\frac{t}{\beta} + 1 \right)^{1 - \alpha} - 1 \right) $$ - -DFOP: - -$$c_\textrm{twa} = \frac{c_0}{t} \left( - \frac{g}{k_1} \left( 1 - e^{- k_1 t} \right) + - \frac{1-g}{k_2} \left( 1 - e^{- k_2 t} \right) \right) $$ - -Often, the ratio between the time weighted average concentration $c_\textrm{twa}$ -and the initial concentration $c_0$ - -$$f_\textrm{twa} = \frac{c_\textrm{twa}}{c_0}$$ - -is needed. This can be calculated from the fitted initial concentration $c_0$ and -the time weighted average concentration $c_\textrm{twa}$, or directly from -the model parameters using the following formulas: - -SFO: - -$$f_\textrm{twa} = \frac{\left( 1 - e^{- k t} \right)}{k t} $$ - -FOMC: - -$$f_\textrm{twa} = \frac{\beta}{t (1 - \alpha)} - \left( \left(\frac{t}{\beta} + 1 \right)^{1 - \alpha} - 1 \right) $$ - -DFOP: - -$$f_\textrm{twa} = \frac{1}{t} \left( - \frac{g}{k_1} \left( 1 - e^{- k_1 t} \right) + - \frac{1-g}{k_2} \left( 1 - e^{- k_2 t} \right) \right) $$ - -- cgit v1.2.1