Wissenschaftlicher Berater, Kronacher Str. 12, 79639 Grenzach-Wyhlen, Germany
Privatdozent at the University of Bremen

The data

The following code defines the example dataset from Appendix 7 to the FOCUS kinetics report (FOCUS Work Group on Degradation Kinetics 2014, 354).

library(mkin, quiet = TRUE)
LOD = 0.5
FOCUS_2006_Z = data.frame(
  t = c(0, 0.04, 0.125, 0.29, 0.54, 1, 2, 3, 4, 7, 10, 14, 21,
        42, 61, 96, 124),
  Z0 = c(100, 81.7, 70.4, 51.1, 41.2, 6.6, 4.6, 3.9, 4.6, 4.3, 6.8,
         2.9, 3.5, 5.3, 4.4, 1.2, 0.7),
  Z1 = c(0, 18.3, 29.6, 46.3, 55.1, 65.7, 39.1, 36, 15.3, 5.6, 1.1,
         1.6, 0.6, 0.5 * LOD, NA, NA, NA),
  Z2 = c(0, NA, 0.5 * LOD, 2.6, 3.8, 15.3, 37.2, 31.7, 35.6, 14.5,
         0.8, 2.1, 1.9, 0.5 * LOD, NA, NA, NA),
  Z3 = c(0, NA, NA, NA, NA, 0.5 * LOD, 9.2, 13.1, 22.3, 28.4, 32.5,
         25.2, 17.2, 4.8, 4.5, 2.8, 4.4))

FOCUS_2006_Z_mkin <- mkin_wide_to_long(FOCUS_2006_Z)

Parent and one metabolite

The next step is to set up the models used for the kinetic analysis. As the simultaneous fit of parent and the first metabolite is usually straightforward, Step 1 (SFO for parent only) is skipped here. We start with the model 2a, with formation and decline of metabolite Z1 and the pathway from parent directly to sink included (default in mkin).

Z.2a <- mkinmod(Z0 = mkinsub("SFO", "Z1"),
                Z1 = mkinsub("SFO"))
## Successfully compiled differential equation model from auto-generated C code.
m.Z.2a <- mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE)
plot_sep(m.Z.2a)