Check compiled mkinmod versions in examples and tests

Tests all pass (Linux)

5 files changed, 56 insertions, 7 deletions

diff --git a/R/mkinfit.R b/R/mkinfit.R
index b0df6e8c..38f76674 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -28,6 +28,7 @@ mkinfit <- function(mkinmod, observed,
   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(),

@@ -263,6 +264,7 @@ mkinfit <- function(mkinmod, observed,
     out <- mkinpredict(mkinmod, parms, 

                        odeini, outtimes, 

                        solution_type = solution_type, 

+                       use_compiled = use_compiled,

                        method.ode = method.ode,

                        atol = atol, rtol = rtol, ...)

 

@@ -282,6 +284,7 @@ mkinfit <- function(mkinmod, observed,
         out_plot <- mkinpredict(mkinmod, parms,

                                 odeini, outtimes_plot, 

                                 solution_type = solution_type, 

+                                use_compiled = use_compiled,

                                 method.ode = method.ode,

                                 atol = atol, rtol = rtol, ...)

 

diff --git a/R/mkinpredict.R b/R/mkinpredict.R
index bed82441..864eefbe 100644
--- a/R/mkinpredict.R
+++ b/R/mkinpredict.R
@@ -19,6 +19,7 @@
 
 mkinpredict <- function(mkinmod, odeparms, odeini, 
 			outtimes, solution_type = "deSolve", 
+      use_compiled = "auto",
 			method.ode = "lsoda", atol = 1e-8, rtol = 1e-10,
 			map_output = TRUE, ...) {
 
@@ -87,7 +88,7 @@ mkinpredict <- function(mkinmod, odeparms, odeini,
     names(out) <- c("time", mod_vars)
   } 
   if (solution_type == "deSolve") {
-    if (!is.null(mkinmod$compiled)) {
+    if (!is.null(mkinmod$compiled) & use_compiled[1] != FALSE) {
        mkindiff <- mkinmod$compiled
      } else {
        mkindiff <- function(t, state, parms) {
diff --git a/inst/unitTests/runit.mkinerrmin.R b/inst/unitTests/runit.mkinerrmin.R
index 56a33ff9..96793a36 100644
--- a/inst/unitTests/runit.mkinerrmin.R
+++ b/inst/unitTests/runit.mkinerrmin.R
@@ -8,26 +8,34 @@ test.FOCUS_2006_D_SFO_SFO <- function()
          m1 = list(type = "SFO"), use_of_ff = "max")
 
   fit.1.e <- mkinfit(SFO_SFO.1, FOCUS_2006_D)
-  fit.1.d <- mkinfit(SFO_SFO.1, solution_type = "deSolve", FOCUS_2006_D)
+  fit.1.d <- mkinfit(SFO_SFO.1, solution_type = "deSolve", use_compiled = FALSE, FOCUS_2006_D)
+  fit.1.dc <- mkinfit(SFO_SFO.1, solution_type = "deSolve", use_compiled = TRUE, FOCUS_2006_D)
   fit.2.e <- mkinfit(SFO_SFO.2, FOCUS_2006_D)
-  fit.2.d <- mkinfit(SFO_SFO.2, solution_type = "deSolve", FOCUS_2006_D)
+  fit.2.d <- mkinfit(SFO_SFO.2, solution_type = "deSolve", use_compiled = FALSE, FOCUS_2006_D)
+  fit.2.dc <- mkinfit(SFO_SFO.2, solution_type = "deSolve", use_compiled = TRUE, FOCUS_2006_D)
 
   FOCUS_2006_D_results_schaefer07_means <- c(
     parent_0 = 99.65, DT50_parent = 7.04, DT50_m1 = 131.34)
 
   r.1.e <- c(fit.1.e$bparms.optim[[1]], endpoints(fit.1.e)$distimes[[1]])
   r.1.d <- c(fit.1.d$bparms.optim[[1]], endpoints(fit.1.d)$distimes[[1]])
+  r.1.dc <- c(fit.1.dc$bparms.optim[[1]], endpoints(fit.1.dc)$distimes[[1]])
   r.2.e <- c(fit.2.e$bparms.optim[[1]], endpoints(fit.2.e)$distimes[[1]])
   r.2.d <- c(fit.2.d$bparms.optim[[1]], endpoints(fit.2.d)$distimes[[1]])
+  r.2.dc <- c(fit.2.dc$bparms.optim[[1]], endpoints(fit.2.dc)$distimes[[1]])
 
   dev.1.e <- 100 * (r.1.e - FOCUS_2006_D_results_schaefer07_means)/r.1.e 
   checkIdentical(as.numeric(abs(dev.1.e)) < 1, rep(TRUE, 3))
   dev.1.d <- 100 * (r.1.d - FOCUS_2006_D_results_schaefer07_means)/r.1.d 
   checkIdentical(as.numeric(abs(dev.1.d)) < 1, rep(TRUE, 3))
+  dev.1.dc <- 100 * (r.1.dc - FOCUS_2006_D_results_schaefer07_means)/r.1.dc 
+  checkIdentical(as.numeric(abs(dev.1.dc)) < 1, rep(TRUE, 3))
   dev.2.e <- 100 * (r.2.e - FOCUS_2006_D_results_schaefer07_means)/r.2.e 
   checkIdentical(as.numeric(abs(dev.2.e)) < 1, rep(TRUE, 3))
   dev.2.d <- 100 * (r.2.d - FOCUS_2006_D_results_schaefer07_means)/r.2.d 
   checkIdentical(as.numeric(abs(dev.2.d)) < 1, rep(TRUE, 3))
+  dev.2.dc <- 100 * (r.2.dc - FOCUS_2006_D_results_schaefer07_means)/r.2.dc 
+  checkIdentical(as.numeric(abs(dev.2.d)) < 1, rep(TRUE, 3))
 
   round(mkinerrmin(fit.2.e), 4)
   round(mkinerrmin(fit.2.d), 4)
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 }