+ - - - - - -

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")
-print(FOCUS_2006_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

print(FOCUS_2006_D)

##      name time  value
 ## 1  parent    0  99.46
 ## 2  parent    0 102.04
@@ -262,62 +118,30 @@ print(FOCUS_2006_D)
 ## 41     m1  100  31.04
 ## 42     m1  100  33.13
 ## 43     m1  120  25.15
-## 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 -the gcc compiler 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"))
-

- -

## Compiling differential equation model from auto-generated C code...
-

- -

print(SFO_SFO$diffs)
-

- +## 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 the gcc compiler 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"))

## Compiling differential equation model from auto-generated C code...

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"
-

- +## "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)
-

- -

A plot of the fit including a residual plot for both observed variables is obtained -using the plot method for mkinfit objects.

- -

plot(fit, show_residuals = TRUE)
-

- -

plot of chunk unnamed-chunk-5

- +

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 method for mkinfit objects.

plot(fit, show_residuals = TRUE)

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

- -

mkinparplot(fit)
-

- -

plot of chunk unnamed-chunk-6

- -

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

- -

summary(fit)
-

- -

## mkin version:    0.9.36 
+mkinparplot(fit)
+
+A comprehensive report of the results is obtained using the summary method for mkinfit objects.
+summary(fit)
+## mkin version:    0.9.37 
 ## R version:       3.2.1 
-## Date of fit:     Sun Jun 21 18:14:52 2015 
-## Date of summary: Sun Jun 21 18:14:52 2015 
+## Date of fit:     Mon Jun 22 18:45:34 2015 
+## Date of summary: Mon Jun 22 18:45:34 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -325,7 +149,7 @@ objects.
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.733 s
+## Fitted with method Port using 153 model solutions performed in 0.609 s
 ## 
 ## Weighting: none
 ## 
@@ -435,9 +259,20 @@ objects.
 ##   100       m1    31.04 3.198e+01 -9.416e-01
 ##   100       m1    33.13 3.198e+01  1.148e+00
 ##   120       m1    25.15 2.879e+01 -3.640e+00
-##   120       m1    33.31 2.879e+01  4.520e+00
-
+##   120       m1    33.31 2.879e+01  4.520e+00

- +

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

2015-06-22

Example evaluation of FOCUS Example Dataset D