From ec9e65053b214fa30e8b947ccbc47930eeaa01a4 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 16 Apr 2015 11:00:53 +0200
Subject: Check compiled mkinmod versions in examples and tests

Tests all pass (Linux)
---
 man/mkinpredict.Rd | 24 +++++++++++++++++++++++-
 1 file changed, 23 insertions(+), 1 deletion(-)

(limited to 'man/mkinpredict.Rd')

diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd
index 7d8979e4..7450a7ce 100644
--- a/man/mkinpredict.Rd
+++ b/man/mkinpredict.Rd
@@ -10,7 +10,8 @@
 }
 \usage{
   mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = "deSolve",
-	      method.ode = "lsoda", atol = 1e-08, rtol = 1e-10, map_output = TRUE, ...)
+	      method.ode = "lsoda", use_compiled = "auto", atol = 1e-08, rtol = 1e-10,
+        map_output = TRUE, ...)
 }
 \arguments{
   \item{mkinmod}{
@@ -41,6 +42,10 @@
     \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}{
     Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-8,
     lower than in \code{\link{lsoda}}.
@@ -70,6 +75,8 @@
 	      solution_type = "analytical")
   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")
 
@@ -92,5 +99,20 @@
   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"))
+  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,]))
+  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,]))
+  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,]))
 }
 \keyword{ manip }
-- 
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