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

Abstract

In the regulatory evaluation of chemical substances like plant protection products (pesticides), biocides and other chemicals, degradation data play an important role. For the evaluation of pesticide degradation experiments, detailed guidance has been developed, based on nonlinear optimisation. The R add-on package mkin (Ranke 2016) implements fitting some of the models recommended in this guidance from within R and calculates some statistical measures for data series within one or more compartments, for parent and metabolites.

library(mkin)
# Define the kinetic model
m_SFO_SFO_SFO <- mkinmod(parent = mkinsub("SFO", "M1"),
                         M1 = mkinsub("SFO", "M2"),
                         M2 = mkinsub("SFO"),
                         use_of_ff = "max", quiet = TRUE)


# Produce model predictions using some arbitrary parameters
sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
d_SFO_SFO_SFO <- mkinpredict(m_SFO_SFO_SFO,
  c(k_parent = 0.03,
    f_parent_to_M1 = 0.5, k_M1 = log(2)/100,
    f_M1_to_M2 = 0.9, k_M2 = log(2)/50),
  c(parent = 100, M1 = 0, M2 = 0),
  sampling_times)

# Generate a dataset by adding normally distributed errors with
# standard deviation 3, for two replicates at each sampling time
d_SFO_SFO_SFO_err <- add_err(d_SFO_SFO_SFO, reps = 2,
                             sdfunc = function(x) 3,
                             n = 1, seed = 123456789 )

# Fit the model to the dataset
f_SFO_SFO_SFO <- mkinfit(m_SFO_SFO_SFO, d_SFO_SFO_SFO_err[[1]], quiet = TRUE)

# Plot the results separately for parent and metabolites
plot_sep(f_SFO_SFO_SFO, lpos = c("topright", "bottomright", "bottomright"))