From 3ee58ca030d5c9e6bffb71f1e2bd7fca0f355b61 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 4 Dec 2013 05:35:46 +0100
Subject: Make clear in help file that gmkin is experimental

---
 man/gmkin.Rd | 3 +++
 1 file changed, 3 insertions(+)

(limited to 'man')

diff --git a/man/gmkin.Rd b/man/gmkin.Rd
index 29a4f8c..8a7d132 100644
--- a/man/gmkin.Rd
+++ b/man/gmkin.Rd
@@ -8,6 +8,9 @@
   \href{http://github.com/jverzani/gWidgetsWWW2}{github page of gWidgetsWWW2} 
   for an explanation how this toolkit works.
 }
+\note{
+  This GUI is experimental and not recommended for real work.
+}
 \usage{
   gmkin()
 }
-- 
cgit v1.2.1


From 8b94131388071980e62c17190eb4229e89975a0c Mon Sep 17 00:00:00 2001
From: = <=>
Date: Wed, 4 Dec 2013 10:25:14 +0100
Subject: Make it possible to use different ode solvers

---
 man/mkinfit.Rd     |  6 ++++++
 man/mkinpredict.Rd | 17 +++++++++++------
 2 files changed, 17 insertions(+), 6 deletions(-)

(limited to 'man')

diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index 51e26ed..0c5d76a 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -20,6 +20,7 @@ mkinfit(mkinmod, observed,
   state.ini = c(100, rep(0, length(mkinmod$diffs) - 1)), 
   fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1], 
   solution_type = "auto",
+  method.ode = "lsoda",
   method.modFit = "Marq",
   control.modFit = list(),
   plot = FALSE, quiet = FALSE, err = NULL, weight = "none", 
@@ -85,6 +86,11 @@ mkinfit(mkinmod, observed,
     dependence of degradation rates and metabolites). This argument is passed
     on to the helper function \code{\link{mkinpredict}}.
   }
+  \item{method.ode}{
+    The solution method passed via \code{\link{mkinpredict}} to
+    \code{\link{ode}} in case the solution type is "deSolve". The default
+    "lsoda" is performant, but sometimes fails to converge.
+  }
   \item{method.modFit}{
     The optimisation method passed to \code{\link{modFit}}. The default "Marq"
     is the Levenberg Marquardt algorithm \code{\link{nls.lm}} from the package
diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd
index afb57e0..97db90e 100644
--- a/man/mkinpredict.Rd
+++ b/man/mkinpredict.Rd
@@ -10,7 +10,7 @@
 }
 \usage{
   mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = "deSolve",
-	      map_output = TRUE, atol = 1e-08, rtol = 1e-10, ...)
+	      method.ode = "lsoda", atol = 1e-08, rtol = 1e-10, map_output = TRUE, ...)
 }
 \arguments{
   \item{mkinmod}{
@@ -33,12 +33,13 @@
     The method that should be used for producing the predictions. This should
     generally be "analytical" if there is only one observed variable, and
     usually "deSolve" in the case of several observed variables. The third
-    possibility "eigen" is faster but produces results that the author believes
-    to be less accurate.
+    possibility "eigen" is faster but not applicable to some models e.g.
+    using FOMC for the parent compound.
   }
-  \item{map_output}{
-    Boolean to specify if the output should list values for the observed
-    variables (default) or for all state variables (if set to FALSE). 
+  \item{method.ode}{
+    The solution method passed via \code{\link{mkinpredict}} to
+    \code{\link{ode}} in case the solution type is "deSolve". The default
+    "lsoda" is performant, but sometimes fails to converge.
   }
   \item{atol}{
     Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-8,
@@ -48,6 +49,10 @@
     Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-10,
     much lower than in \code{\link{lsoda}}.
   }
+  \item{map_output}{
+    Boolean to specify if the output should list values for the observed
+    variables (default) or for all state variables (if set to FALSE). 
+  }
   \item{\dots}{
     Further arguments passed to the ode solver in case such a solver is used.
   }
-- 
cgit v1.2.1