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Diffstat (limited to 'R/mkinmod.R')
| -rw-r--r-- | R/mkinmod.R | 65 |
1 files changed, 39 insertions, 26 deletions
diff --git a/R/mkinmod.R b/R/mkinmod.R index e58d1e22..a410c02d 100644 --- a/R/mkinmod.R +++ b/R/mkinmod.R @@ -1,26 +1,34 @@ #' Function to set up a kinetic model with one or more state variables #' -#' 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. +#' This function is usually called using a call to [mkinsub()] for each observed +#' variable, specifying the corresponding submodel as well as outgoing pathways +#' (see examples). #' #' For the definition of model types and their parameters, the equations given #' in the FOCUS and NAFTA guidance documents are used. #' -#' @param ... 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" +#' For kinetic models with more than one observed variable, a symbolic solution +#' of the system of differential equations is included in the resulting +#' mkinmod object in some cases, speeding up the solution. +#' +#' If a C compiler is found by [pkgbuild::has_compiler()] and there +#' is more than one observed variable in the specification, C code is generated +#' for evaluating the differential equations, compiled using +#' [inline::cfunction()] and added to the resulting mkinmod object. +#' +#' @param ... For each observed variable, a list as obtained by [mkinsub()] +#' has to be specified as an argument (see examples). 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", "HS" and "logistic" +#' can additionally be chosen for the first variable which is assumed to be +#' the source compartment. +#' Additionally, [mkinsub()] has an argument \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. +#' additional [mkinsub()] argument can be \code{sink = FALSE}, effectively +#' fixing the flux to sink to zero. #' @param 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 @@ -30,12 +38,12 @@ #' submodel types and pathways can be given as a single list using this #' argument. Default is NULL. #' @param quiet Should messages be suppressed? -#' @param verbose If \code{TRUE}, passed to \code{\link{cfunction}} if +#' @param verbose If \code{TRUE}, passed to [inline::cfunction()] if #' applicable to give detailed information about the C function being built. #' @importFrom methods signature #' @importFrom pkgbuild has_compiler #' @importFrom inline cfunction -#' @return A list of class \code{mkinmod} for use with \code{\link{mkinfit}}, +#' @return A list of class \code{mkinmod} for use with [mkinfit()], #' containing, among others, #' \item{diffs}{ #' A vector of string representations of differential equations, one for @@ -61,8 +69,8 @@ #' returned by cfunction. #' } #' @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}}. +#' model for metabolites, you may want to read the note in the help +#' page to [mkinfit]. #' @author Johannes Ranke #' @references FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence #' and Degradation Kinetics from Environmental Fate Studies on Pesticides in @@ -93,16 +101,21 @@ #' parent = mkinsub("SFO", "m1"), #' m1 = mkinsub("SFO"), verbose = TRUE) #' +#' # The symbolic solution which is available in this case is not +#' # made for human reading but for speed of computation +#' SFO_SFO$deg_func +#' #' # If we have several parallel metabolites #' # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R) -#' m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")), -#' M1 = mkinsub("SFO"), -#' M2 = mkinsub("SFO"), -#' use_of_ff = "max", quiet = TRUE) +#' m_synth_DFOP_par <- mkinmod( +#' parent = mkinsub("DFOP", c("M1", "M2")), +#' M1 = mkinsub("SFO"), +#' M2 = mkinsub("SFO"), +#' use_of_ff = "max", quiet = TRUE) #' #' fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, -#' synthetic_data_for_UBA_2014[[12]]$data, -#' quiet = TRUE) +#' synthetic_data_for_UBA_2014[[12]]$data, +#' quiet = TRUE) #' } #' #' @export mkinmod |