Laboratory Data L1

The following code defines example dataset L1 from the FOCUS kinetics report, p. 284:

library("mkin", quietly = TRUE)
FOCUS_2006_L1 = data.frame(
  t = rep(c(0, 1, 2, 3, 5, 7, 14, 21, 30), each = 2),
  parent = c(88.3, 91.4, 85.6, 84.5, 78.9, 77.6,
             72.0, 71.9, 50.3, 59.4, 47.0, 45.1,
             27.7, 27.3, 10.0, 10.4, 2.9, 4.0))
FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)

Here we use the assumptions of simple first order (SFO), the case of declining rate constant over time (FOMC) and the case of two different phases of the kinetics (DFOP). For a more detailed discussion of the models, please see the FOCUS kinetics report.

Since mkin version 0.9-32 (July 2014), we can use shorthand notation like "SFO" for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.

m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet = TRUE)
summary(m.L1.SFO)
## mkin version:    0.9.46.3 
## R version:       3.4.2 
## Date of fit:     Thu Nov 16 17:14:44 2017 
## Date of summary: Thu Nov 16 17:14:44 2017 
## 
## Equations:
## d_parent/dt = - k_parent_sink * parent
## 
## Model predictions using solution type analytical 
## 
## Fitted with method Port using 37 model solutions performed in 0.252 s
## 
## Weighting: none
## 
## Starting values for parameters to be optimised:
##               value   type
## parent_0      89.85  state
## k_parent_sink  0.10 deparm
## 
## Starting values for the transformed parameters actually optimised:
##                       value lower upper
## parent_0          89.850000  -Inf   Inf
## log_k_parent_sink -2.302585  -Inf   Inf
## 
## Fixed parameter values:
## None
## 
## Optimised, transformed parameters with symmetric confidence intervals:
##                   Estimate Std. Error  Lower  Upper
## parent_0            92.470    1.36800 89.570 95.370
## log_k_parent_sink   -2.347    0.04057 -2.433 -2.261
## 
## Parameter correlation:
##                   parent_0 log_k_parent_sink
## parent_0            1.0000            0.6248
## log_k_parent_sink   0.6248            1.0000
## 
## Residual standard error: 2.948 on 16 degrees of freedom
## 
## 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      92.47000   67.58 2.170e-21 89.57000 95.3700
## k_parent_sink  0.09561   24.65 1.867e-14  0.08773  0.1042
## 
## Chi2 error levels in percent:
##          err.min n.optim df
## All data   3.424       2  7
## parent     3.424       2  7
## 
## Resulting formation fractions:
##             ff
## parent_sink  1
## 
## Estimated disappearance times:
##         DT50  DT90
## parent 7.249 24.08
## 
## Data:
##  time variable observed predicted residual
##     0   parent     88.3    92.471  -4.1710
##     0   parent     91.4    92.471  -1.0710
##     1   parent     85.6    84.039   1.5610
##     1   parent     84.5    84.039   0.4610
##     2   parent     78.9    76.376   2.5241
##     2   parent     77.6    76.376   1.2241
##     3   parent     72.0    69.412   2.5884
##     3   parent     71.9    69.412   2.4884
##     5   parent     50.3    57.330  -7.0301
##     5   parent     59.4    57.330   2.0699
##     7   parent     47.0    47.352  -0.3515
##     7   parent     45.1    47.352  -2.2515
##    14   parent     27.7    24.247   3.4528
##    14   parent     27.3    24.247   3.0528
##    21   parent     10.0    12.416  -2.4163
##    21   parent     10.4    12.416  -2.0163
##    30   parent      2.9     5.251  -2.3513
##    30   parent      4.0     5.251  -1.2513

A plot of the fit is obtained with the plot function for mkinfit objects.

plot(m.L1.SFO, show_errmin = TRUE, main = "FOCUS L1 - SFO")

The residual plot can be easily obtained by

mkinresplot(m.L1.SFO, ylab = "Observed", xlab = "Time")