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)
##      name time  value
## 1  parent    0  99.46
## 2  parent    0 102.04
## 3  parent    1  93.50
## 4  parent    1  92.50
## 5  parent    3  63.23
## 6  parent    3  68.99
## 7  parent    7  52.32
## 8  parent    7  55.13
## 9  parent   14  27.27
## 10 parent   14  26.64
## 11 parent   21  11.50
## 12 parent   21  11.64
## 13 parent   35   2.85
## 14 parent   35   2.91
## 15 parent   50   0.69
## 16 parent   50   0.63
## 17 parent   75   0.05
## 18 parent   75   0.06
## 19 parent  100     NA
## 20 parent  100     NA
## 21 parent  120     NA
## 22 parent  120     NA
## 23     m1    0   0.00
## 24     m1    0   0.00
## 25     m1    1   4.84
## 26     m1    1   5.64
## 27     m1    3  12.91
## 28     m1    3  12.96
## 29     m1    7  22.97
## 30     m1    7  24.47
## 31     m1   14  41.69
## 32     m1   14  33.21
## 33     m1   21  44.37
## 34     m1   21  46.44
## 35     m1   35  41.22
## 36     m1   35  37.95
## 37     m1   50  41.19
## 38     m1   50  40.01
## 39     m1   75  40.09
## 40     m1   75  33.85
## 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 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"))
## Successfully compiled 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"

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

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"))

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

## Warning in summary.mkinfit(object): Could not calculate correlation; no
## covariance matrix

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

summary(fit)
## Warning in summary.mkinfit(fit): Could not calculate correlation; no
## covariance matrix
## mkin version used for fitting:    0.9.49.4 
## R version used for fitting:       3.6.0 
## Date of fit:     Tue May  7 08:09:11 2019 
## Date of summary: Tue May  7 08:09:11 2019 
## 
## Equations:
## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
## d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1
## 
## Model predictions using solution type deSolve 
## 
## Fitted using 153 model solutions performed in 0.398 s
## 
## Error model:
## Constant variance 
## 
## Starting values for parameters to be optimised:
##                    value   type
## parent_0      100.750000  state
## k_parent_sink   0.100000 deparm
## k_parent_m1     0.100100 deparm
## k_m1_sink       0.100200 deparm
## sigma           3.125504  error
## 
## Starting values for the transformed parameters actually optimised:
##                        value lower upper
## parent_0          100.750000  -Inf   Inf
## log_k_parent_sink  -2.302585  -Inf   Inf
## log_k_parent_m1    -2.301586  -Inf   Inf
## log_k_m1_sink      -2.300587  -Inf   Inf
## sigma               3.125504     0   Inf
## 
## Fixed parameter values:
##      value  type
## m1_0     0 state
## 
## Optimised, transformed parameters with symmetric confidence intervals:
##                   Estimate Std. Error Lower Upper
## parent_0            99.600         NA    NA    NA
## log_k_parent_sink   -3.038         NA    NA    NA
## log_k_parent_m1     -2.980         NA    NA    NA
## log_k_m1_sink       -5.248         NA    NA    NA
## sigma                3.126         NA    NA    NA
## 
## Parameter correlation:
## No covariance matrix
## Backtransformed parameters:
## Confidence intervals for internally transformed parameters are asymmetric.
## t-test (unrealistically) based on the assumption of normal distribution
## for estimators of untransformed parameters.
##                Estimate t value Pr(>t) Lower Upper
## parent_0      99.600000      NA     NA    NA    NA
## k_parent_sink  0.047920      NA     NA    NA    NA
## k_parent_m1    0.050780      NA     NA    NA    NA
## k_m1_sink      0.005261      NA     NA    NA    NA
## sigma          3.126000      NA     NA    NA    NA
## 
## FOCUS Chi2 error levels in percent:
##          err.min n.optim df
## All data   6.398       4 15
## parent     6.827       3  6
## m1         4.490       1  9
## 
## Resulting formation fractions:
##                 ff
## parent_sink 0.4855
## parent_m1   0.5145
## m1_sink     1.0000
## 
## Estimated disappearance times:
##           DT50   DT90
## parent   7.023  23.33
## m1     131.761 437.70
## 
## Data:
##  time variable observed predicted   residual
##     0   parent    99.46  99.59848 -1.385e-01
##     0   parent   102.04  99.59848  2.442e+00
##     1   parent    93.50  90.23787  3.262e+00
##     1   parent    92.50  90.23787  2.262e+00
##     3   parent    63.23  74.07320 -1.084e+01
##     3   parent    68.99  74.07320 -5.083e+00
##     7   parent    52.32  49.91207  2.408e+00
##     7   parent    55.13  49.91207  5.218e+00
##    14   parent    27.27  25.01257  2.257e+00
##    14   parent    26.64  25.01257  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
##    35   parent     2.91   3.14787 -2.379e-01
##    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 -7.382e-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
##    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
##   120       m1    25.15  28.78984 -3.640e+00
##   120       m1    33.31  28.78984  4.520e+00