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Diffstat (limited to 'man/mkinmod.Rd')
| -rw-r--r-- | man/mkinmod.Rd | 65 |
1 files changed, 39 insertions, 26 deletions
diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd index 6a6d2027..98623201 100644 --- a/man/mkinmod.Rd +++ b/man/mkinmod.Rd @@ -13,19 +13,19 @@ mkinmod( ) } \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" +\item{...}{For each observed variable, a list as obtained by \code{\link[=mkinsub]{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, \code{\link[=mkinsub]{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 \code{\link[=mkinsub]{mkinsub()}} argument can be \code{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 @@ -39,11 +39,11 @@ argument. Default is NULL.} \item{quiet}{Should messages be suppressed?} -\item{verbose}{If \code{TRUE}, passed to \code{\link{cfunction}} if +\item{verbose}{If \code{TRUE}, passed to \code{\link[inline:cfunction]{inline::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}}, +A list of class \code{mkinmod} for use with \code{\link[=mkinfit]{mkinfit()}}, containing, among others, \item{diffs}{ A vector of string representations of differential equations, one for @@ -70,19 +70,27 @@ returned by cfunction. } } \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. +This function is usually called using a call to \code{\link[=mkinsub]{mkinsub()}} for each observed +variable, specifying the corresponding submodel as well as outgoing pathways +(see examples). } \details{ For the definition of model types and their parameters, the equations given in the FOCUS and NAFTA guidance documents are used. + +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 \code{\link[pkgbuild:has_compiler]{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 +\code{\link[inline:cfunction]{inline::cfunction()}} and added to the resulting mkinmod object. } \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 \link{mkinfit}. } \examples{ @@ -105,16 +113,21 @@ SFO_SFO <- mkinmod( 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) } } |