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-rw-r--r--R/mkinmod.R18
1 files changed, 12 insertions, 6 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"),

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