From 0a3eb0893cb4bd1b12f07a79069d1c7f5e991495 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 25 Oct 2019 00:37:42 +0200 Subject: Use roxygen for functions and methods --- man/mkinmod.Rd | 238 +++++++++++++++++++++++++++++---------------------------- 1 file changed, 123 insertions(+), 115 deletions(-) (limited to 'man/mkinmod.Rd') diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd index 62b02775..91f285e2 100644 --- a/man/mkinmod.Rd +++ b/man/mkinmod.Rd @@ -1,115 +1,123 @@ -\name{mkinmod} -\alias{mkinmod} -\title{ - 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{ -mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verbose = FALSE) -} -\arguments{ - \item{...}{ - For each observed variable, a list has to be specified as an argument, containing - at least a component \code{type}, specifying the type of kinetics to use - for the variable. Currently, single first order kinetics "SFO", - indeterminate order rate equation kinetics "IORE", or - single first order with reversible binding "SFORB" are implemented for all - variables, while - "FOMC", "DFOP" and "HS" can additionally be chosen for the first - variable which is assumed to be the source compartment. - Additionally, each component of the list can include a character vector \code{to}, - specifying names of variables to which a transfer is to be assumed in the - model. - If the argument \code{use_of_ff} is set to "min" (default) and the model for - the compartment is "SFO" or "SFORB", an additional component of the list - can be "sink=FALSE" effectively fixing the flux to sink to zero. - } - \item{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. - } - \item{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. - } - \item{quiet}{ - Should messages be suppressed? - } - \item{verbose}{ - If \code{TRUE}, passed to \code{\link{cfunction}} if applicable to give - detailed information about the C function being built. - } -} -\value{ - A list of class \code{mkinmod} for use with \code{\link{mkinfit}}, containing - \item{diffs}{ A vector of string representations of differential equations, - one for each modelling variable. } - \item{parms}{ A vector of parameter names occurring in the differential equations. } - \item{map}{ A list containing named character vectors for each observed variable, specifying - the modelling variables by which it is represented. } - \item{use_of_ff}{ The content of \code{use_of_ff} is passed on in this list component. } - \item{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 - \code{\link{mkinfit}}. -} -\references{ - FOCUS (2006) \dQuote{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, - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} - - NAFTA Technical Working Group on Pesticides (not dated) Guidance for - Evaluating and Calculating Degradation Kinetics in Environmental - Media -} -\author{ - Johannes Ranke -} -\examples{ -# 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")) - -\dontrun{ -# 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) -} -} -\keyword{ models } +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/mkinmod.R +\name{mkinmod} +\alias{mkinmod} +\title{Function to set up a kinetic model with one or more state variables} +\usage{ +mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, + verbose = FALSE) +} +\arguments{ +\item{...}{For each observed variable, a list has to be specified as an +argument, containing at least a component \code{type}, specifying the type +of kinetics to use for the variable. Currently, single first order +kinetics "SFO", indeterminate order rate equation kinetics "IORE", or +single first order with reversible binding "SFORB" are implemented for all +variables, while "FOMC", "DFOP" and "HS" can additionally be chosen for +the first variable which is assumed to be the source compartment. +Additionally, each component of the list can include a character vector +\code{to}, specifying names of variables to which a transfer is to be +assumed in the model. If the argument \code{use_of_ff} is set to "min" +(default) and the model for the compartment is "SFO" or "SFORB", an +additional component of the list can be "sink=FALSE" effectively fixing +the flux to sink to zero.} + +\item{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.} + +\item{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.} + +\item{quiet}{Should messages be suppressed?} + +\item{verbose}{If \code{TRUE}, passed to \code{\link{cfunction}} if +applicable to give detailed information about the C function being built.} +} +\value{ +A list of class \code{mkinmod} for use with \code{\link{mkinfit}}, + containing, among others, + \item{diffs}{ + A vector of string representations of differential equations, one for + each modelling variable. + } + \item{map}{ + A list containing named character vectors for each observed variable, + specifying the modelling variables by which it is represented. + } + \item{use_of_ff}{ + The content of \code{use_of_ff} is passed on in this list component. + } + \item{coefmat}{ + The coefficient matrix, if the system of differential equations can be + represented by one. + } + \item{ll}{ + The likelihood function, taking the parameter vector as the first argument. + } +} +\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. +} +\details{ +For the definition of model types and their parameters, the equations given +in the FOCUS and NAFTA guidance documents are used. +} +\note{ +The IORE submodel is not well tested for metabolites. When using this + model for metabolites, you may want to read the second note in the help + page to \code{\link{mkinfit}}. +} +\examples{ + +# 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")) + +\dontrun{ +# 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) +} + +} +\references{ +FOCUS (2006) \dQuote{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, + \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} + + NAFTA Technical Working Group on Pesticides (not dated) Guidance for + Evaluating and Calculating Degradation Kinetics in Environmental Media +} +\author{ +Johannes Ranke +} -- cgit v1.2.1