diff options
Diffstat (limited to 'man/mkinfit.Rd')
| -rw-r--r-- | man/mkinfit.Rd | 24 |
1 files changed, 6 insertions, 18 deletions
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index b4923ddd..f3ce6a08 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -21,9 +21,8 @@ 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", "odeintr"), 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(), @@ -103,11 +102,6 @@ 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}}. @@ -175,12 +169,13 @@ mkinfit(mkinmod, observed, according to the number of observations. } \item{atol}{ - Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-8, - lower than in \code{\link{lsoda}}. + Absolute error tolerance, passed to \code{\link{ode}} when the solution + type is "deSolve". Default is 1e-8, lower than in \code{\link{lsoda}}. } \item{rtol}{ - Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-10, - much lower than in \code{\link{lsoda}}. + Absolute error tolerance, passed to \code{\link{ode}} when the solution + type is "deSolve". Default is 1e-10, much lower than in + \code{\link{lsoda}}. } \item{n.outtimes}{ The length of the dataseries that is produced by the model prediction @@ -246,13 +241,6 @@ print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = TRUE))) coef(fit) endpoints(fit) -\dontrun{ -# deSolve is slower when ccSolve is not installed and set up -print(system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D, - solution_type = "deSolve"))) -coef(fit.deSolve) -endpoints(fit.deSolve) -} # Use stepwise fitting, using optimised parameters from parent only fit, FOMC \dontrun{ |