Depend on parallel, doc improvements

By depending on parallel instead of importing it, functions to set up
and stop a cluster are always available when mkin is loaded.

The use of multicore processing in mmkin on Windows is now documented in
the help file, which brings mkin closer to a version 1.0 #9.

1 files changed, 50 insertions, 7 deletions

diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd
index 98623201..e5b1c8f3 100644
--- a/man/mkinmod.Rd
+++ b/man/mkinmod.Rd
@@ -1,7 +1,9 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mkinmod.R
+% Please edit documentation in R/mkinmod.R, R/mkinsub.R
 \name{mkinmod}
 \alias{mkinmod}
+\alias{print.mkinmod}
+\alias{mkinsub}
 \title{Function to set up a kinetic model with one or more state variables}
 \usage{
 mkinmod(
@@ -11,6 +13,10 @@ mkinmod(
   quiet = FALSE,
   verbose = FALSE
 )
+
+\method{print}{mkinmod}(x, ...)
+
+mkinsub(submodel, to = NULL, sink = TRUE, full_name = NA)
 }
 \arguments{
 \item{...}{For each observed variable, a list as obtained by \code{\link[=mkinsub]{mkinsub()}}
@@ -25,13 +31,14 @@ variables to which a transfer is to be assumed in the model.
 If the argument \code{use_of_ff} is set to "min"
 (default) and the model for the compartment is "SFO" or "SFORB", an
 additional \code{\link[=mkinsub]{mkinsub()}} argument can be \code{sink = FALSE}, effectively
-fixing the flux to sink to zero.}
+fixing the flux to sink to zero.
+In print.mkinmod, this argument is currently not used.}
 
 \item{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.}
 
 \item{speclist}{The specification of the observed variables and their
 submodel types and pathways can be given as a single list using this
@@ -41,6 +48,22 @@ 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{x}{An \code{\link{mkinmod}} object.}
+
+\item{submodel}{Character vector of length one to specify the submodel type.
+See \code{\link{mkinmod}} for the list of allowed submodel names.}
+
+\item{to}{Vector of the names of the state variable to which a
+transformation shall be included in the model.}
+
+\item{sink}{Should a pathway to sink be included in the model in addition to
+the pathways to other state variables?}
+
+\item{full_name}{An optional name to be used e.g. for plotting fits
+performed with the model.  You can use non-ASCII characters here, but then
+your R code will not be portable, \emph{i.e.} may produce unintended plot
+results on other operating systems or system configurations.}
 }
 \value{
 A list of class \code{mkinmod} for use with \code{\link[=mkinfit]{mkinfit()}},
@@ -68,11 +91,19 @@ represented by one.
 If generated, a compiled function calculating the derivatives as
 returned by cfunction.
 }
+
+A list for use with \code{\link{mkinmod}}.
 }
 \description{
 This function is usually called using a call to \code{\link[=mkinsub]{mkinsub()}} for each observed
 variable, specifying the corresponding submodel as well as outgoing pathways
 (see examples).
+
+Print mkinmod objects in a way that the user finds his way to get to its
+components.
+
+This is a convenience function to set up the lists used as arguments for
+\code{\link{mkinmod}}.
 }
 \details{
 For the definition of model types and their parameters, the equations given
@@ -103,6 +134,11 @@ SFO_SFO <- mkinmod(
   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"),
@@ -123,13 +159,20 @@ m_synth_DFOP_par <- mkinmod(
  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,
   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