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/mkinfit.Rd | 24 ++++++------------------
 1 file changed, 6 insertions(+), 18 deletions(-)

(limited to 'man/mkinfit.Rd')

diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index b4923ddd..f3ce6a08 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -21,9 +21,8 @@ mkinfit(mkinmod, observed,
   parms.ini = "auto",
   state.ini = "auto",
   fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1], 
-  solution_type = c("auto", "analytical", "eigen", "deSolve"),
+  solution_type = c("auto", "analytical", "eigen", "deSolve", "odeintr"),
   method.ode = "lsoda",
-  use_compiled = "auto",
   method.modFit = c("Port", "Marq", "SANN", "Nelder-Mead", "BFGS", "CG", "L-BFGS-B"),
   maxit.modFit = "auto",
   control.modFit = list(),
@@ -103,11 +102,6 @@ mkinfit(mkinmod, observed,
     \code{\link{ode}} in case the solution type is "deSolve". The default
     "lsoda" is performant, but sometimes fails to converge.
   }
-  \item{use_compiled}{
-    If set to \code{FALSE}, no compiled version of the \code{\link{mkinmod}} 
-    model is used, in the calls to \code{\link{mkinpredict}} even if
-    a compiled verion is present. 
-  }
   \item{method.modFit}{
     The optimisation method passed to \code{\link{modFit}}.  
 
@@ -175,12 +169,13 @@ mkinfit(mkinmod, observed,
     according to the number of observations.
   }
   \item{atol}{
-    Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-8,
-    lower than in \code{\link{lsoda}}.
+    Absolute error tolerance, passed to \code{\link{ode}} when the solution
+    type is "deSolve". Default is 1e-8, lower than in \code{\link{lsoda}}.
   }
   \item{rtol}{
-    Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-10,
-    much lower than in \code{\link{lsoda}}.
+    Absolute error tolerance, passed to \code{\link{ode}} when the solution
+    type is "deSolve". Default is 1e-10, much lower than in
+    \code{\link{lsoda}}.
   }
   \item{n.outtimes}{
     The length of the dataseries that is produced by the model prediction
@@ -246,13 +241,6 @@ print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D,
                            solution_type = "eigen", quiet = TRUE)))
 coef(fit)
 endpoints(fit)
-\dontrun{
-# deSolve is slower when ccSolve is not installed and set up
-print(system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D, 
-                           solution_type = "deSolve")))
-coef(fit.deSolve)
-endpoints(fit.deSolve)
-}
 
 # Use stepwise fitting, using optimised parameters from parent only fit, FOMC
 \dontrun{
-- 
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