Check compiled mkinmod versions in examples and tests

Tests all pass (Linux)

2 files changed, 41 insertions, 4 deletions

diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index 4b0ad1a7..4250bfda 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -23,6 +23,7 @@ mkinfit(mkinmod, observed,
   fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1], 
   solution_type = "auto",
   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(),
@@ -102,6 +103,10 @@ 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, even if is present. 
+  }
   \item{method.modFit}{
     The optimisation method passed to \code{\link{modFit}}.  
 
@@ -235,9 +240,18 @@ SFO_SFO <- mkinmod(
   parent = list(type = "SFO", to = "m1", sink = TRUE),
   m1 = list(type = "SFO"))
 # Fit the model to the FOCUS example dataset D using defaults
-fit <- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen")
-fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve")
-summary(fit)
+system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen"))
+system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", use_compiled = FALSE))
+system.time(fit.deSolve.compiled <- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", use_compiled = TRUE))
+# The performance benefit of using the compiled version is immense compared with deSolve without compilation, and
+# about a factor of two compared with the eigenvalue based solution
+coef(fit)
+coef(fit.deSolve)
+coef(fit.deSolve.compiled)
+endpoints(fit)
+endpoints(fit.deSolve)
+# Check compiled model versions against other solutions
+
 
 # Use stepwise fitting, using optimised parameters from parent only fit, FOMC
 \dontrun{
@@ -289,6 +303,7 @@ f.w.man.irls <- mkinfit(SFO_SFO.ff, dw, err = "err.man",
                        reweight.method = "obs")
 summary(f.w.man.irls)
 }
+
 }
 \keyword{ models }
 \keyword{ optimize }
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}}.
@@ -71,6 +76,8 @@
   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 }