# Function to set up a kinetic model with one or more state variables

### Description

The function usually takes several expressions, each assigning a compound name to a list, specifying the kinetic model type and reaction or transfer to other observed compartments. Instead of specifying several expressions, a list of lists can be given in the speclist argument.

For the definition of model types and their parameters, the equations given in the FOCUS and NAFTA guidance documents are used.

### Usage

1 |

### Arguments

`...` |
For each observed variable, a list has to be specified as an argument, containing
at least a component |

`use_of_ff` |
Specification of the use of formation fractions in the model equations and, if applicable, the coefficient matrix. If "min", a minimum use of formation fractions is made in order to avoid fitting the product of formation fractions and rate constants. If "max", formation fractions are always used. |

`speclist` |
The specification of the observed variables and their submodel types and pathways can be given as a single list using this argument. Default is NULL. |

`quiet` |
Should messages be suppressed? |

`verbose` |
If |

### Value

A list of class `mkinmod`

for use with `mkinfit`

, containing

`diffs` |
A vector of string representations of differential equations, one for each modelling variable. |

`parms` |
A vector of parameter names occurring in the differential equations. |

`map` |
A list containing named character vectors for each observed variable, specifying the modelling variables by which it is represented. |

`use_of_ff` |
The content of |

`coefmat` |
The coefficient matrix, if the system of differential equations can be represented by one. |

### Note

The IORE submodel is not well tested (yet). When using this model for metabolites,
you may want to read the second note in the help page to
`mkinfit`

.

### Author(s)

Johannes Ranke

### References

FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, http://focus.jrc.ec.europa.eu/dk

NAFTA Technical Working Group on Pesticides (not dated) Guidance for Evaluating and Calculating Degradation Kinetics in Environmental Media

### Examples

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | ```
# Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)
SFO <- mkinmod(parent = list(type = "SFO"))
# One parent compound, one metabolite, both single first order
SFO_SFO <- mkinmod(
parent = mkinsub("SFO", "m1"),
m1 = mkinsub("SFO"))
## Not run:
# The above model used to be specified like this, before the advent of mkinsub()
SFO_SFO <- mkinmod(
parent = list(type = "SFO", to = "m1"),
m1 = list(type = "SFO"))
# Show details of creating the C function
SFO_SFO <- mkinmod(
parent = mkinsub("SFO", "m1"),
m1 = mkinsub("SFO"), verbose = TRUE)
# If we have several parallel metabolites
# (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)
m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
M1 = mkinsub("SFO"),
M2 = mkinsub("SFO"),
use_of_ff = "max", quiet = TRUE)
fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par,
synthetic_data_for_UBA_2014[[12]]$data,
quiet = TRUE)
## End(Not run)
``` |