Make it possible to use different ode solvers

2 files changed, 17 insertions, 6 deletions

diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index 51e26ed5..0c5d76a9 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 afb57e0b..97db90e3 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.
   }