Here we get a performance benefit of a factor of 8 using the version of the differential equation model compiled from C code!

Abstract

@@ -147,7 +140,7 @@ f_SFO_SFO_SFO <- documentation page and manual for further information.

A further graphical user interface (GUI) that has recently been brought to a decent degree of maturity is the browser based GUI named gmkin. Please see its documentation page and manual for further information.

- - - - - - - - - - - -

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.

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).

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.

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.

mkinparplot(fit)

mkinparplot(fit)

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

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 () {
 
 
 
-

Abstract

In the regulatory evaluation of chemical substances like plant protection products (pesticides), biocides and other chemicals, degradation data play an important role. For the evaluation of pesticide degradation experiments, detailed guidance has been developed, based on nonlinear optimisation. The R add-on package mkin (Ranke 2016) implements fitting some of the models recommended in this guidance from within R and calculates some statistical measures for data series within one or more compartments, for parent and metabolites.

library(mkin)

## Loading required package: minpack.lm

## Loading required package: rootSolve

## Loading required package: inline

## Loading required package: methods

## Loading required package: parallel

# Define the kinetic model
+library(mkin)
+# Define the kinetic model
 m_SFO_SFO_SFO <- mkinmod(parent = mkinsub("SFO", "M1"),
                          M1 = mkinsub("SFO", "M2"),
                          M2 = mkinsub("SFO"),
@@ -276,7 +271,7 @@ f_SFO_SFO_SFO <- mkinfit(m_SFO_SFO_SFO, d_SFO_SFO_SFO_err[[1]], quiet = TRUE)
 
 # Plot the results separately for parent and metabolites
 plot_sep(f_SFO_SFO_SFO, lpos = c("topright", "bottomright", "bottomright"))
-
+

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

2017-09-14

2017-11-16

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

2017-09-14

2017-11-16

Example evaluation of FOCUS dataset Z

Johannes Ranke

2017-09-14

2017-11-16

The data

Performance benefit by using compiled model definitions in mkin

Johannes Ranke

2017-09-14

2017-11-16

Articles version 0.9.46.1

Articles version 0.9.46.3

Introduction to mkin

Johannes Ranke

2017-09-14

2017-11-16

Abstract

diff --git a/docs/articles/twa.html b/docs/articles/twa.html index 3a1d5731..0a4df0ff 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -62,14 +62,7 @@ News - - - - - - - - +

Calculation of time weighted average concentrations with mkin

Johannes Ranke

2017-09-14

2017-11-16

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

2017-07-21

2017-11-16

Example evaluation of FOCUS dataset Z

Johannes Ranke

2017-09-14

2017-11-16

The data

Introduction to mkin

Johannes Ranke

2017-07-21

2017-11-16

Abstract

Background

Recent developments

diff --git a/docs/articles/twa.html b/docs/articles/twa.html index 3a1d5731..0a4df0ff 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -62,14 +62,7 @@ News -
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