Further formatting improvement of benchmark vignette

Also, use .rmd extension instead of .Rmd for vignettes.

1 files changed, 0 insertions, 79 deletions

diff --git a/vignettes/twa.Rmd b/vignettes/twa.Rmd
deleted file mode 100644
index 6f283eb2..00000000
--- a/vignettes/twa.Rmd
+++ /dev/null
@@ -1,79 +0,0 @@
----
-title: Calculation of time weighted average concentrations with mkin
-author: Johannes Ranke
-date: "`r Sys.Date()`"
-bibliography: references.bib
-output: rmarkdown::html_vignette
-vignette: >
-  %\VignetteIndexEntry{Calculation of time weighted average concentrations with mkin}
-  %\VignetteEngine{knitr::rmarkdown}
-  %\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. 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 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:
-
-$$c_\textrm{twa} = \frac{c_0}{t} \left(
-  \frac{g}{k_1} \left( 1 - e^{- k_1 t} \right) +
-  \frac{1-g}{k_2} \left( 1 - e^{- k_2 t} \right)  \right) $$
-
-HS for $t > t_b$:
-
-$$c_\textrm{twa} = \frac{c_0}{t} \left(
-  \frac{1}{k_1} \left( 1 - e^{- k_1 t_b} \right) +
-  \frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)} \right)  \right) $$
-
-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:
-
-$$f_\textrm{twa} = \frac{1}{t} \left(
-  \frac{g}{k_1} \left( 1 - e^{- k_1 t} \right) +
-  \frac{1-g}{k_2} \left( 1 - e^{- k_2 t} \right)  \right) $$
-
-HS for $t > t_b$:
-
-$$f_\textrm{twa} = \frac{1}{t} \left(
-  \frac{1}{k_1} \left( 1 - e^{- k_1 t_b} \right) +
-  \frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)} \right)  \right) $$
-
-Note that a method for calculating maximum moving window time weighted average
-concentrations for a model fitted by 'mkinfit' or from parent decline model
-parameters is included in the `max_twa_parent()` function. If the same is
-needed for metabolites, the function `pfm::max_twa()` from the 'pfm' package
-can be used.