+ +

@@ -111,8 +112,9 @@

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
@@ -160,31 +162,35 @@
 ## 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 * parent" 
 ##                                                        m1 
 ## "d_m1 = + f_parent_to_m1 * k_parent * parent - k_m1 * 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)

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

## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Shapiro-Wilk test for
-## standardized residuals: p = 0.0165

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:    0.9.50.3 
-## R version used for fitting:       4.0.2 
-## Date of fit:     Thu Oct  8 09:14:03 2020 
-## Date of summary: Thu Oct  8 09:14:03 2020 
++summary(fit)
+## mkin version used for fitting:    0.9.50.4 
+## R version used for fitting:       4.0.3 
+## Date of fit:     Thu Nov 19 15:00:06 2020 
+## Date of summary: Thu Nov 19 15:00:06 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -192,7 +198,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 421 model solutions performed in 0.171 s
+## Fitted using 401 model solutions performed in 0.188 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -206,11 +212,11 @@
 ## f_parent_to_m1   0.5000 deparm
 ## 
 ## Starting values for the transformed parameters actually optimised:
-##                     value lower upper
-## parent_0       100.750000  -Inf   Inf
-## log_k_parent    -2.302585  -Inf   Inf
-## log_k_m1        -2.301586  -Inf   Inf
-## f_parent_ilr_1   0.000000  -Inf   Inf
+##                      value lower upper
+## parent_0        100.750000  -Inf   Inf
+## log_k_parent     -2.302585  -Inf   Inf
+## log_k_m1         -2.301586  -Inf   Inf
+## f_parent_qlogis   0.000000  -Inf   Inf
 ## 
 ## Fixed parameter values:
 ##      value  type
@@ -219,7 +225,6 @@
 ## 
 ## Warning(s): 
 ## Observations with value of zero were removed from the data
-## Shapiro-Wilk test for standardized residuals: p =  0.0165
 ## 
 ## Results:
 ## 
@@ -227,20 +232,20 @@
 ##   204.4486 212.6365 -97.22429
 ## 
 ## Optimised, transformed parameters with symmetric confidence intervals:
-##                Estimate Std. Error    Lower    Upper
-## parent_0       99.60000    1.57000 96.40000 102.8000
-## log_k_parent   -2.31600    0.04087 -2.39900  -2.2330
-## log_k_m1       -5.24800    0.13320 -5.51800  -4.9770
-## f_parent_ilr_1  0.04096    0.06312 -0.08746   0.1694
-## sigma           3.12600    0.35850  2.39600   3.8550
+##                 Estimate Std. Error   Lower    Upper
+## parent_0        99.60000    1.57000 96.4000 102.8000
+## log_k_parent    -2.31600    0.04087 -2.3990  -2.2330
+## log_k_m1        -5.24700    0.13320 -5.5180  -4.9770
+## f_parent_qlogis  0.05792    0.08926 -0.1237   0.2395
+## sigma            3.12600    0.35850  2.3960   3.8550
 ## 
 ## Parameter correlation:
-##                  parent_0 log_k_parent   log_k_m1 f_parent_ilr_1      sigma
-## parent_0        1.000e+00    5.174e-01 -1.688e-01     -5.471e-01 -3.214e-07
-## log_k_parent    5.174e-01    1.000e+00 -3.263e-01     -5.426e-01  3.168e-07
-## log_k_m1       -1.688e-01   -3.263e-01  1.000e+00      7.478e-01 -1.410e-07
-## f_parent_ilr_1 -5.471e-01   -5.426e-01  7.478e-01      1.000e+00  5.093e-10
-## sigma          -3.214e-07    3.168e-07 -1.410e-07      5.093e-10  1.000e+00
+##                   parent_0 log_k_parent   log_k_m1 f_parent_qlogis      sigma
+## parent_0         1.000e+00    5.174e-01 -1.688e-01      -5.471e-01 -1.171e-06
+## log_k_parent     5.174e-01    1.000e+00 -3.263e-01      -5.426e-01 -8.481e-07
+## log_k_m1        -1.688e-01   -3.263e-01  1.000e+00       7.478e-01  8.209e-07
+## f_parent_qlogis -5.471e-01   -5.426e-01  7.478e-01       1.000e+00  1.305e-06
+## sigma           -1.171e-06   -8.481e-07  8.209e-07       1.305e-06  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -277,10 +282,10 @@
 ##     1   parent    92.50  90.23787  2.262e+00
 ##     3   parent    63.23  74.07319 -1.084e+01
 ##     3   parent    68.99  74.07319 -5.083e+00
-##     7   parent    52.32  49.91206  2.408e+00
-##     7   parent    55.13  49.91206  5.218e+00
-##    14   parent    27.27  25.01257  2.257e+00
-##    14   parent    26.64  25.01257  1.627e+00
+##     7   parent    52.32  49.91207  2.408e+00
+##     7   parent    55.13  49.91207  5.218e+00
+##    14   parent    27.27  25.01258  2.257e+00
+##    14   parent    26.64  25.01258  1.627e+00
 ##    21   parent    11.50  12.53462 -1.035e+00
 ##    21   parent    11.64  12.53462 -8.946e-01
 ##    35   parent     2.85   3.14787 -2.979e-01
@@ -288,25 +293,25 @@
 ##    50   parent     0.69   0.71624 -2.624e-02
 ##    50   parent     0.63   0.71624 -8.624e-02
 ##    75   parent     0.05   0.06074 -1.074e-02
-##    75   parent     0.06   0.06074 -7.381e-04
+##    75   parent     0.06   0.06074 -7.382e-04
 ##     1       m1     4.84   4.80296  3.704e-02
 ##     1       m1     5.64   4.80296  8.370e-01
 ##     3       m1    12.91  13.02400 -1.140e-01
 ##     3       m1    12.96  13.02400 -6.400e-02
 ##     7       m1    22.97  25.04476 -2.075e+00
 ##     7       m1    24.47  25.04476 -5.748e-01
-##    14       m1    41.69  36.69002  5.000e+00
-##    14       m1    33.21  36.69002 -3.480e+00
+##    14       m1    41.69  36.69003  5.000e+00
+##    14       m1    33.21  36.69003 -3.480e+00
 ##    21       m1    44.37  41.65310  2.717e+00
 ##    21       m1    46.44  41.65310  4.787e+00
-##    35       m1    41.22  43.31312 -2.093e+00
-##    35       m1    37.95  43.31312 -5.363e+00
-##    50       m1    41.19  41.21831 -2.831e-02
-##    50       m1    40.01  41.21831 -1.208e+00
-##    75       m1    40.09  36.44703  3.643e+00
-##    75       m1    33.85  36.44703 -2.597e+00
-##   100       m1    31.04  31.98163 -9.416e-01
-##   100       m1    33.13  31.98163  1.148e+00
+##    35       m1    41.22  43.31313 -2.093e+00
+##    35       m1    37.95  43.31313 -5.363e+00
+##    50       m1    41.19  41.21832 -2.832e-02
+##    50       m1    40.01  41.21832 -1.208e+00
+##    75       m1    40.09  36.44704  3.643e+00
+##    75       m1    33.85  36.44704 -2.597e+00
+##   100       m1    31.04  31.98162 -9.416e-01
+##   100       m1    33.13  31.98162  1.148e+00
 ##   120       m1    25.15  28.78984 -3.640e+00
 ##   120       m1    33.31  28.78984  4.520e+00


@@ -324,7 +329,7 @@


 
 
-  Site built with pkgdown 1.5.1.
+  Site built with pkgdown 1.6.1.
 
 
       
-- 
cgit v1.2.1

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

2020-10-08

2020-11-19