diff options
Diffstat (limited to 'man/mkinmod.Rd')
| -rw-r--r-- | man/mkinmod.Rd | 31 |
1 files changed, 15 insertions, 16 deletions
diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd index e5b1c8f3..f71ebfb3 100644 --- a/man/mkinmod.Rd +++ b/man/mkinmod.Rd @@ -9,9 +9,11 @@ mkinmod( ..., use_of_ff = "max", + name = NULL, speclist = NULL, quiet = FALSE, - verbose = FALSE + verbose = FALSE, + cf_dir = NULL ) \method{print}{mkinmod}(x, ...) @@ -40,6 +42,8 @@ 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{name}{A name for the model. Should be a valid R object name.} + \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.} @@ -49,6 +53,9 @@ 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{cf_dir}{Directory where CFunc objects should be saved. Specifying +'cf_dir' without specifying a 'name' for the object is an error.} + \item{x}{An \code{\link{mkinmod}} object.} \item{submodel}{Character vector of length one to specify the submodel type. @@ -113,7 +120,6 @@ 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. @@ -132,17 +138,17 @@ SFO <- mkinmod(parent = mkinsub("SFO")) SFO_SFO <- mkinmod( parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) +print(SFO_SFO) \dontrun{ -# Now supplying full names used for plotting + fit_sfo_sfo <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, solution_type = "deSolve") + + # Now supplying full names used for plotting, and write to user defined location 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"), - m1 = list(type = "SFO")) + m1 = mkinsub("SFO", full_name = "Metabolite M1"), + name = "SFOSFO", cf_dir = tempdir()) +fit_sfo_sfo <- mkinfit(SFO_SFO.2, FOCUS_2006_D, quiet = TRUE, solution_type = "deSolve") # Show details of creating the C function SFO_SFO <- mkinmod( @@ -166,13 +172,6 @@ fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, 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 |