diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/mkinmod.R | 18 | ||||
| -rw-r--r-- | R/mkinsub.R | 20 | ||||
| -rw-r--r-- | R/mmkin.R | 11 |
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) { @@ -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 |