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-rw-r--r--man/mkinmod.Rd57
1 files changed, 50 insertions, 7 deletions
diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd
index 98623201..e5b1c8f3 100644
--- a/man/mkinmod.Rd
+++ b/man/mkinmod.Rd
@@ -1,7 +1,9 @@
% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mkinmod.R
+% Please edit documentation in R/mkinmod.R, R/mkinsub.R
\name{mkinmod}
\alias{mkinmod}
+\alias{print.mkinmod}
+\alias{mkinsub}
\title{Function to set up a kinetic model with one or more state variables}
\usage{
mkinmod(
@@ -11,6 +13,10 @@ mkinmod(
quiet = FALSE,
verbose = FALSE
)
+
+\method{print}{mkinmod}(x, ...)
+
+mkinsub(submodel, to = NULL, sink = TRUE, full_name = NA)
}
\arguments{
\item{...}{For each observed variable, a list as obtained by \code{\link[=mkinsub]{mkinsub()}}
@@ -25,13 +31,14 @@ 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 \code{\link[=mkinsub]{mkinsub()}} argument can be \code{sink = FALSE}, effectively
-fixing the flux to sink to zero.}
+fixing the flux to sink to zero.
+In print.mkinmod, this argument is currently not used.}
\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.}
+model equations and, if applicable, the coefficient matrix. If "max",
+formation fractions are always used (default). If "min", a minimum use of
+formation fractions is made, i.e. each pathway to a metabolite has its
+own rate constant.}
\item{speclist}{The specification of the observed variables and their
submodel types and pathways can be given as a single list using this
@@ -41,6 +48,22 @@ argument. Default is NULL.}
\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.}
+
+\item{x}{An \code{\link{mkinmod}} object.}
+
+\item{submodel}{Character vector of length one to specify the submodel type.
+See \code{\link{mkinmod}} for the list of allowed submodel names.}
+
+\item{to}{Vector of the names of the state variable to which a
+transformation shall be included in the model.}
+
+\item{sink}{Should a pathway to sink be included in the model in addition to
+the pathways to other state variables?}
+
+\item{full_name}{An optional name to be used e.g. for plotting fits
+performed with the model. You can use non-ASCII characters here, but then
+your R code will not be portable, \emph{i.e.} may produce unintended plot
+results on other operating systems or system configurations.}
}
\value{
A list of class \code{mkinmod} for use with \code{\link[=mkinfit]{mkinfit()}},
@@ -68,11 +91,19 @@ represented by one.
If generated, a compiled function calculating the derivatives as
returned by cfunction.
}
+
+A list for use with \code{\link{mkinmod}}.
}
\description{
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).
+
+Print mkinmod objects in a way that the user finds his way to get to its
+components.
+
+This is a convenience function to set up the lists used as arguments for
+\code{\link{mkinmod}}.
}
\details{
For the definition of model types and their parameters, the equations given
@@ -103,6 +134,11 @@ SFO_SFO <- mkinmod(
m1 = mkinsub("SFO"))
\dontrun{
+# Now supplying full names used for plotting
+ SFO_SFO.2 <- mkinmod(
+ parent = mkinsub("SFO", "m1", full_name = "Test compound"),
+ m1 = mkinsub("SFO", full_name = "Metabolite M1"))
+
# The above model used to be specified like this, before the advent of mkinsub()
SFO_SFO <- mkinmod(
parent = list(type = "SFO", to = "m1"),
@@ -123,13 +159,20 @@ m_synth_DFOP_par <- mkinmod(
parent = mkinsub("DFOP", c("M1", "M2")),
M1 = mkinsub("SFO"),
M2 = mkinsub("SFO"),
- use_of_ff = "max", quiet = TRUE)
+ quiet = TRUE)
fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par,
synthetic_data_for_UBA_2014[[12]]$data,
quiet = TRUE)
}
+
+ m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),
+ M1 = list(type = "SFO", to = "M2"),
+ M2 = list(type = "SFO"), use_of_ff = "max")
+
+ print(m_synth_SFO_lin)
+
}
\references{
FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence

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