diff options
Diffstat (limited to 'man/mkinfit.Rd')
| -rw-r--r-- | man/mkinfit.Rd | 30 |
1 files changed, 26 insertions, 4 deletions
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index 9c82f5ff..801f540c 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -21,8 +21,9 @@ mkinfit(mkinmod, observed, parms.ini = "auto", state.ini = "auto", fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1], - solution_type = "auto", + 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"), maxit.modFit = "auto", control.modFit = list(), @@ -102,6 +103,11 @@ 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, in the calls to \code{\link{mkinpredict}} even if + a compiled verion is present. + } \item{method.modFit}{ The optimisation method passed to \code{\link{modFit}}. @@ -235,8 +241,22 @@ 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) -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{ @@ -258,10 +278,10 @@ SFORB_SFO <- mkinmod( m1 = list(type = "SFO")) # Fit the model to the FOCUS example dataset D using defaults fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D) +fit.SFORB_SFO.deSolve <- mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSolve") # Use starting parameters from parent only SFORB fit (not really needed in this case) fit.SFORB = mkinfit(SFORB, FOCUS_2006_D) fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode) -} # Weighted fits, including IRLS SFO_SFO.ff <- mkinmod(parent = list(type = "SFO", to = "m1"), @@ -275,6 +295,7 @@ summary(f.w.mean) f.w.mean.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", reweight.method = "obs") summary(f.w.mean.irls) +} \dontrun{ # Manual weighting @@ -287,6 +308,7 @@ f.w.man.irls <- mkinfit(SFO_SFO.ff, dw, err = "err.man", reweight.method = "obs") summary(f.w.man.irls) } + } \keyword{ models } \keyword{ optimize } |