Example evaluation of FOCUS Example Dataset D

@@ -100,8 +107,8 @@

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 at 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, quietly = TRUE)
-print(FOCUS_2006_D)

library(mkin, quietly = TRUE)
+print(FOCUS_2006_D)

##      name time  value
 ## 1  parent    0  99.46
 ## 2  parent    0 102.04
@@ -149,29 +156,29 @@
 ## 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)

## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
-## value of zero were removed from the data

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

## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with value
+## of zero were removed from the data

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 used for fitting:    0.9.49.6 
-## R version used for fitting:       3.6.1 
-## Date of fit:     Fri Nov  1 10:10:44 2019 
-## Date of summary: Fri Nov  1 10:10:44 2019 
+summary(fit)
+## mkin version used for fitting:    0.9.49.11 
+## R version used for fitting:       4.0.0 
+## Date of fit:     Thu May  7 08:59:27 2020 
+## Date of summary: Thu May  7 08:59:27 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -179,7 +186,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted using 389 model solutions performed in 1.015 s
+## Fitted using 389 model solutions performed in 1.031 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -212,18 +219,18 @@
 ## sigma                3.126    0.35850  2.396   3.855
 ## 
 ## Parameter correlation:
-##                     parent_0 log_k_parent_sink log_k_parent_m1
-## parent_0           1.000e+00         6.067e-01      -6.372e-02
-## log_k_parent_sink  6.067e-01         1.000e+00      -8.550e-02
-## log_k_parent_m1   -6.372e-02        -8.550e-02       1.000e+00
-## log_k_m1_sink     -1.688e-01        -6.252e-01       4.731e-01
-## sigma              1.164e-09        -8.908e-10       1.652e-08
-##                   log_k_m1_sink      sigma
-## parent_0             -1.688e-01  1.164e-09
-## log_k_parent_sink    -6.252e-01 -8.908e-10
-## log_k_parent_m1       4.731e-01  1.652e-08
-## log_k_m1_sink         1.000e+00 -1.340e-10
-## sigma                -1.340e-10  1.000e+00
+##                     parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+## parent_0           1.000e+00         6.067e-01      -6.372e-02    -1.688e-01
+## log_k_parent_sink  6.067e-01         1.000e+00      -8.550e-02    -6.252e-01
+## log_k_parent_m1   -6.372e-02        -8.550e-02       1.000e+00     4.731e-01
+## log_k_m1_sink     -1.688e-01        -6.252e-01       4.731e-01     1.000e+00
+## sigma              5.287e-10         3.306e-09       4.421e-08    -3.319e-10
+##                        sigma
+## parent_0           5.287e-10
+## log_k_parent_sink  3.306e-09
+## log_k_parent_m1    4.421e-08
+## log_k_m1_sink     -3.319e-10
+## sigma              1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -295,7 +302,7 @@
 ##   120       m1    33.31  28.78984  4.520e+00


 
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       All vignettes
       
 
-      
-        Example evaluation of FOCUS Example Dataset D
-        Example evaluation of FOCUS Laboratory Data L1 to L3
-        Introduction to mkin
-        Calculation of time weighted average concentrations with mkin
-        Example evaluation of FOCUS dataset Z
-        Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance
-        Benchmark timings for mkin on various systems
-        Performance benefit by using compiled model definitions in mkin
-      
+      
+        Example evaluation of FOCUS Example Dataset D
+        
+        
Example evaluation of FOCUS Laboratory Data L1 to L3
+        
+        
Introduction to mkin
+        
+        
Calculation of time weighted average concentrations with mkin
+        
+        
Example evaluation of FOCUS dataset Z
+        
+        
Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance
+        
+        
Benchmark timings for mkin on various systems
+        
+        
Performance benefit by using compiled model definitions in mkin
+        
+

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

2019-11-01

2020-05-07

All vignettes