From ec574cff822a1238138c0aa69b3d1459bdc3dfa8 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 19 Jun 2015 17:46:11 +0200
Subject: Use odeintr instead of ccSolve for compiling models

---
 man/mkinmod.Rd | 34 ++++++++++++++++++++++++++++++++--
 1 file changed, 32 insertions(+), 2 deletions(-)

(limited to 'man/mkinmod.Rd')

diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd
index f6a8fe5d..c5d59403 100644
--- a/man/mkinmod.Rd
+++ b/man/mkinmod.Rd
@@ -11,9 +11,16 @@
 
   For the definition of model types and their parameters, the equations given
   in the FOCUS and NAFTA guidance documents are used.
+
+  When a C++ compiler is available (currently checking for g++), the model is
+  compiled using the \code{\link{odeintr}} package, so that model fitting will
+  be faster.
 }
 \usage{
-mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE)
+mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE,
+        odeintr_compile = c("auto", "no", "yes"),
+        odeintr_method = "rk5_i",
+        odeintr_atol = 1e-8, odeintr_rtol = 1e-10)
 }
 \arguments{
   \item{...}{
@@ -45,6 +52,24 @@ mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE)
   \item{quiet}{
     Should messages be suppressed?
   }
+  \item{odeintr_compile}{
+    When "no", the model is not compiled using \code{\link{compile_sys}}.
+    When "auto", it is only compiled when an eigenvalue based solution
+    is not possible, as compiling the model takes some time and we 
+    want to avoid this in case it does not bring a large performance benefit.
+  }
+  \item{odeintr_method}{
+    The integration method passed to \code{\link{compile_sys}}. The default "rk5_i"
+    is an interpolating adaptive method.
+  }
+  \item{odeintr_atol}{
+    Absolute error tolerance, only used when the model is compiled using the odeintr
+    package. Default is 1e-8, lower than in \code{\link{compile_sys}}.
+  }
+  \item{odeintr_rtol}{
+    Relative error tolerance, only used when the model is compiled using the odeintr
+    package. Default is 1e-10, lower than in \code{\link{compile_sys}}.
+  }
 }
 \value{
   A list of class \code{mkinmod} for use with \code{\link{mkinfit}}, containing 
@@ -56,6 +81,11 @@ mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE)
     \item{use_of_ff}{ The content of \code{use_of_ff} is passed on in this list component. }
     \item{coefmat}{ The coefficient matrix, if the system of differential equations can be
       represented by one. }
+    \item{e}{An environment where the functions generated by \{code\{link{compile_sys}}
+      are installed when the model is compiled. The name used for the model is "m", so
+      for example the function for setting parameters is e$m_set_params(). See
+      the help page for \code{\link{compile_sys}} for the available functions
+      and their arguments.
 }
 \note{
   The IORE submodel is not well tested (yet). When using this model for metabolites, 
@@ -92,12 +122,12 @@ SFO_SFO <- mkinmod(
 
 # If we have several parallel metabolites 
 # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)
+\dontrun{
 m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
                            M1 = mkinsub("SFO"),
                            M2 = mkinsub("SFO"),
                            use_of_ff = "max", quiet = TRUE)
 
-\dontrun{
 fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, 
                           synthetic_data_for_UBA_2014[[12]]$data,
                           quiet = TRUE)
-- 
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