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-rw-r--r--man/mkinmod.Rd31
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

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