1 files changed, 19 insertions, 15 deletions

diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd
index c6aee75f..745f1922 100644
--- a/man/mkinpredict.Rd
+++ b/man/mkinpredict.Rd
@@ -9,9 +9,10 @@
   kinetic parameters and initial values for the state variables.
 }
 \usage{
-  mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = "deSolve",
-	      use_compiled = "auto", method.ode = "lsoda", atol = 1e-08, rtol = 1e-10,
-        map_output = TRUE, ...)
+  mkinpredict(mkinmod, odeparms, odeini, outtimes, 
+              solution_type = c("deSolve", "analytical", "eigen", "odeintr"),
+              method.ode = "lsoda", atol.deSolve = 1e-08, rtol.deSolve = 1e-10,
+              map_output = TRUE, ...)
 }
 \arguments{
   \item{mkinmod}{
@@ -35,22 +36,21 @@
     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 not applicable to some models e.g.
-    using FOMC for the parent compound.
+    using FOMC for the parent compound. If a compiler is installed and functional,
+    method "odeintr" is also available, which is faster for complex models.
+    The default is "deSolve", as it works for all models and does not depend
+    on a compiler to be present.
   }
   \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{use_compiled}{
-    If set to \code{FALSE}, no compiled version of the \code{\link{mkinmod}} 
-    model is used, even if is present. 
-  }
-  \item{atol}{
+  \item{atol.deSolve}{
     Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-8,
     lower than in \code{\link{lsoda}}.
   }
-  \item{rtol}{
+  \item{rtol.deSolve}{
     Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-10,
     much lower than in \code{\link{lsoda}}.
   }
@@ -76,8 +76,6 @@
   mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
 	      solution_type = "deSolve")
   mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
-	      solution_type = "deSolve", use_compiled = FALSE)
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
 	      solution_type = "eigen")
 
 
@@ -99,20 +97,26 @@
   mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 
 	      seq(0, 20, by = 0.01))[2001,]
 
-  # Check compiled model versions - they are faster than the eigenvalue based solutions!
   SFO_SFO = mkinmod(parent = list(type = "SFO", to = "m1"),
                     m1 = list(type = "SFO"))
+  \dontrun{
+  # Check compiled model versions - they are faster than the eigenvalue based solutions!
+  SFO_SFO = mkinmod(parent = list(type = "SFO", to = "m1"),
+                    m1 = list(type = "SFO"), odeintr_compile = "yes")
+  }
   system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "eigen")[201,]))
+  \dontrun{
   system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), 
-                solution_type = "deSolve")[201,]))
+                solution_type = "odeintr")[201,]))
   system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), 
-                solution_type = "deSolve", use_compiled = FALSE)[201,]))
+                solution_type = "deSolve")[201,]))
+  }
 }
 \keyword{ manip }