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-rw-r--r--R/mkinmod.R18
-rw-r--r--R/mkinsub.R20
-rw-r--r--R/mmkin.R11
3 files changed, 24 insertions, 25 deletions
diff --git a/R/mkinmod.R b/R/mkinmod.R
index a410c02d..1af72db5 100644
--- a/R/mkinmod.R
+++ b/R/mkinmod.R
@@ -29,11 +29,12 @@
#' (default) and the model for the compartment is "SFO" or "SFORB", an
#' additional [mkinsub()] argument can be \code{sink = FALSE}, effectively
#' fixing the flux to sink to zero.
+#' In print.mkinmod, this argument is currently not used.
#' @param 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.
#' @param 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.
@@ -91,6 +92,11 @@
#' 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"),
@@ -111,7 +117,7 @@
#' 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,
@@ -451,8 +457,8 @@ mkinmod <- function(..., use_of_ff = "max", speclist = NULL, quiet = FALSE, verb
#' Print mkinmod objects in a way that the user finds his way to get to its
#' components.
#'
+#' @rdname mkinmod
#' @param x An \code{\link{mkinmod}} object.
-#' @param \dots Not used.
#' @examples
#'
#' m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),
diff --git a/R/mkinsub.R b/R/mkinsub.R
index f87c230a..886f712c 100644
--- a/R/mkinsub.R
+++ b/R/mkinsub.R
@@ -3,6 +3,7 @@
#' This is a convenience function to set up the lists used as arguments for
#' \code{\link{mkinmod}}.
#'
+#' @rdname mkinmod
#' @param submodel Character vector of length one to specify the submodel type.
#' See \code{\link{mkinmod}} for the list of allowed submodel names.
#' @param to Vector of the names of the state variable to which a
@@ -14,25 +15,6 @@
#' your R code will not be portable, \emph{i.e.} may produce unintended plot
#' results on other operating systems or system configurations.
#' @return A list for use with \code{\link{mkinmod}}.
-#' @author Johannes Ranke
-#' @examples
-#'
-#' # One parent compound, one metabolite, both single first order.
-#' SFO_SFO <- mkinmod(
-#' parent = list(type = "SFO", to = "m1"),
-#' m1 = list(type = "SFO"))
-#'
-#' # The same model using mkinsub
-#' SFO_SFO.2 <- mkinmod(
-#' parent = mkinsub("SFO", "m1"),
-#' m1 = mkinsub("SFO"))
-#'
-#' \dontrun{
-#' # Now supplying full names
-#' SFO_SFO.2 <- mkinmod(
-#' parent = mkinsub("SFO", "m1", full_name = "Test compound"),
-#' m1 = mkinsub("SFO", full_name = "Metabolite M1"))
-#' }
#' @export
mkinsub <- function(submodel, to = NULL, sink = TRUE, full_name = NA)
{
diff --git a/R/mmkin.R b/R/mmkin.R
index 96453e1d..bb111efe 100644
--- a/R/mmkin.R
+++ b/R/mmkin.R
@@ -60,6 +60,17 @@
#' # Plotting with mmkin (single brackets, extracting an mmkin object) does not
#' # allow to plot the observed variables separately
#' plot(fits.0[1, 1])
+#'
+#' # On Windows, we can use multiple cores by making a cluster using the parallel
+#' # package, which gets loaded with mkin, and passing it to mmkin, e.g.
+#' cl <- makePSOCKcluster(12)
+#' f <- mmkin(c("SFO", "FOMC", "DFOP"),
+#' list(A = FOCUS_2006_A, B = FOCUS_2006_B, C = FOCUS_2006_C, D = FOCUS_2006_D),
+#' cluster = cl, quiet = TRUE)
+#' print(f)
+#' # We get false convergence for the FOMC fit to FOCUS_2006_A because this
+#' # dataset is really SFO, and the FOMC fit is overparameterised
+#' stopCluster(cl)
#' }
#'
#' @export mmkin

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