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authorJohannes Ranke <jranke@uni-bremen.de>2015-04-16 11:00:53 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2015-04-16 11:00:53 +0200
commitec9e65053b214fa30e8b947ccbc47930eeaa01a4 (patch)
tree2328b5015f55363e753f6ca346805ccd75fe0d63 /man/mkinfit.Rd
parent10fb9aac470d87afbe2d4ee9e3d1898bfc3f1aa7 (diff)
Check compiled mkinmod versions in examples and tests
Tests all pass (Linux)
Diffstat (limited to 'man/mkinfit.Rd')
-rw-r--r--man/mkinfit.Rd21
1 files changed, 18 insertions, 3 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 }

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