diff options
Diffstat (limited to 'man/mkinmod.Rd')
| -rw-r--r-- | man/mkinmod.Rd | 34 |
1 files changed, 32 insertions, 2 deletions
diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd index f6a8fe5d..c5d59403 100644 --- a/man/mkinmod.Rd +++ b/man/mkinmod.Rd @@ -11,9 +11,16 @@ For the definition of model types and their parameters, the equations given
in the FOCUS and NAFTA guidance documents are used.
+
+ When a C++ compiler is available (currently checking for g++), the model is
+ compiled using the \code{\link{odeintr}} package, so that model fitting will
+ be faster.
}
\usage{
-mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE)
+mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE,
+ odeintr_compile = c("auto", "no", "yes"),
+ odeintr_method = "rk5_i",
+ odeintr_atol = 1e-8, odeintr_rtol = 1e-10)
}
\arguments{
\item{...}{
@@ -45,6 +52,24 @@ mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE) \item{quiet}{
Should messages be suppressed?
}
+ \item{odeintr_compile}{
+ When "no", the model is not compiled using \code{\link{compile_sys}}.
+ When "auto", it is only compiled when an eigenvalue based solution
+ is not possible, as compiling the model takes some time and we
+ want to avoid this in case it does not bring a large performance benefit.
+ }
+ \item{odeintr_method}{
+ The integration method passed to \code{\link{compile_sys}}. The default "rk5_i"
+ is an interpolating adaptive method.
+ }
+ \item{odeintr_atol}{
+ Absolute error tolerance, only used when the model is compiled using the odeintr
+ package. Default is 1e-8, lower than in \code{\link{compile_sys}}.
+ }
+ \item{odeintr_rtol}{
+ Relative error tolerance, only used when the model is compiled using the odeintr
+ package. Default is 1e-10, lower than in \code{\link{compile_sys}}.
+ }
}
\value{
A list of class \code{mkinmod} for use with \code{\link{mkinfit}}, containing
@@ -56,6 +81,11 @@ mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE) \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{e}{An environment where the functions generated by \{code\{link{compile_sys}}
+ are installed when the model is compiled. The name used for the model is "m", so
+ for example the function for setting parameters is e$m_set_params(). See
+ the help page for \code{\link{compile_sys}} for the available functions
+ and their arguments.
}
\note{
The IORE submodel is not well tested (yet). When using this model for metabolites,
@@ -92,12 +122,12 @@ SFO_SFO <- mkinmod( # If we have several parallel metabolites
# (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)
+\dontrun{
m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
M1 = mkinsub("SFO"),
M2 = mkinsub("SFO"),
use_of_ff = "max", quiet = TRUE)
-\dontrun{
fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par,
synthetic_data_for_UBA_2014[[12]]$data,
quiet = TRUE)
|