diff options
Diffstat (limited to 'man/mkinfit.Rd')
| -rw-r--r-- | man/mkinfit.Rd | 21 |
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 } |