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authorJohannes Ranke <jranke@uni-bremen.de>2015-04-18 00:06:38 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2015-04-18 00:06:38 +0200
commita26b44d15c11ebb41083fc2efab0cc91a027b55b (patch)
tree1ab67782b9f0ec70a2409c430b8f57f32e4d5eb5 /man
parent07685d190e7da7bdc199f0b6cd0bd372c5264aa5 (diff)
Add a vignette showing the performance of compiled models
Diffstat (limited to 'man')
-rw-r--r--man/mkinfit.Rd16
-rw-r--r--man/mkinpredict.Rd2
2 files changed, 11 insertions, 7 deletions
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index 5f43e145..801f540c 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -21,7 +21,7 @@ mkinfit(mkinmod, observed,
parms.ini = "auto",
state.ini = "auto",
fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1],
- solution_type = c("auto", "analytical", "eigen", "deSolve")
+ solution_type = c("auto", "analytical", "eigen", "deSolve"),
method.ode = "lsoda",
use_compiled = "auto",
method.modFit = c("Port", "Marq", "SANN", "Nelder-Mead", "BFGS", "CG", "L-BFGS-B"),
@@ -241,11 +241,15 @@ 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
-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
+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)
diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd
index 7450a7ce..c6aee75f 100644
--- a/man/mkinpredict.Rd
+++ b/man/mkinpredict.Rd
@@ -10,7 +10,7 @@
}
\usage{
mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = "deSolve",
- method.ode = "lsoda", use_compiled = "auto", atol = 1e-08, rtol = 1e-10,
+ use_compiled = "auto", method.ode = "lsoda", atol = 1e-08, rtol = 1e-10,
map_output = TRUE, ...)
}
\arguments{

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