From 1511ed0a775e15ec2158e22d08a4da00cdd834aa Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 16 Nov 2017 17:13:35 +0100 Subject: Use html_vignette for FOCUS_D vignette, fix address Static documentation articles rebuilt by pkgdown::build_articles() --- vignettes/FOCUS_D.html | 179 +++++++++++++++---------------------------------- 1 file changed, 54 insertions(+), 125 deletions(-) (limited to 'vignettes/FOCUS_D.html') diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index 44bbe062..abd7d129 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -8,130 +8,75 @@ + - + Example evaluation of FOCUS Example Dataset D - - - - - - - - - + - - - + - - - - -
- - - - - - - - - - - -

This is just a very simple vignette showing how to fit a degradation model for a parent compound with one transformation product using mkin. After loading the library we look a the data. We have observed concentrations in the column named value at the times specified in column time for the two observed variables named parent and m1.

-
library("mkin")
-
## Loading required package: minpack.lm
-
## Loading required package: rootSolve
-
## Loading required package: inline
-
## Loading required package: methods
-
## Loading required package: parallel
-
print(FOCUS_2006_D)
+
library("mkin")
+print(FOCUS_2006_D)
##      name time  value
 ## 1  parent    0  99.46
 ## 2  parent    0 102.04
@@ -179,27 +124,27 @@ $(document).ready(function () {
 ## 44     m1  120  33.31

Next we specify the degradation model: The parent compound degrades with simple first-order kinetics (SFO) to one metabolite named m1, which also degrades with SFO kinetics.

The call to mkinmod returns a degradation model. The differential equations represented in R code can be found in the character vector $diffs of the mkinmod object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.

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SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
+
SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
## Successfully compiled differential equation model from auto-generated C code.
-
print(SFO_SFO$diffs)
+
print(SFO_SFO$diffs)
##                                                       parent 
 ## "d_parent = - k_parent_sink * parent - k_parent_m1 * parent" 
 ##                                                           m1 
 ##             "d_m1 = + k_parent_m1 * parent - k_m1_sink * m1"

We do the fitting without progress report (quiet = TRUE).

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fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
+
fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)

A plot of the fit including a residual plot for both observed variables is obtained using the plot_sep method for mkinfit objects, which shows separate graphs for all compounds and their residuals.

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plot_sep(fit, lpos = c("topright", "bottomright"))
-

+
plot_sep(fit, lpos = c("topright", "bottomright"))
+

Confidence intervals for the parameter estimates are obtained using the mkinparplot function.

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mkinparplot(fit)
+
mkinparplot(fit)

A comprehensive report of the results is obtained using the summary method for mkinfit objects.

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summary(fit)
-
## mkin version:    0.9.45.2 
-## R version:       3.4.1 
-## Date of fit:     Fri Jul 21 18:02:19 2017 
-## Date of summary: Fri Jul 21 18:02:20 2017 
+
summary(fit)

+
## mkin version:    0.9.46.2 
+## R version:       3.4.2 
+## Date of fit:     Thu Nov 16 17:07:26 2017 
+## Date of summary: Thu Nov 16 17:07:27 2017 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -207,7 +152,7 @@ $(document).ready(function () {
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 1.059 s
+## Fitted with method Port using 153 model solutions performed in 1.031 s
 ## 
 ## Weighting: none
 ## 
@@ -322,21 +267,5 @@ $(document).ready(function () {
 
 
 
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