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Diffstat (limited to 'man/mkinfit.Rd')
| -rw-r--r-- | man/mkinfit.Rd | 24 |
1 files changed, 12 insertions, 12 deletions
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index 21af9a05..c40dff83 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -7,14 +7,10 @@ This function uses the Flexible Modelling Environment package \code{\link{FME}} to create a function calculating the model cost, i.e. the deviation between the kinetic model and the observed data. This model cost is - then minimised using the Levenberg-Marquardt algorithm \code{\link{nls.lm}}, + then minimised using the Port algorithm \code{\link{nlminb}}, using the specified initial or fixed parameters and starting values. Per default, parameters in the kinetic models are internally transformed in order to better satisfy the assumption of a normal distribution of their estimators. - If fitting with transformed fractions leads to a suboptimal fit, doing a - first run without transforming fractions may help. A final - run using the optimised parameters from the previous run as starting values - can then be performed with transformed fractions. In each step of the optimsation, the kinetic model is solved using the function \code{\link{mkinpredict}}. The variance of the residuals for each observed variable can optionally be iteratively reweighted until convergence @@ -27,7 +23,7 @@ mkinfit(mkinmod, observed, fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1], solution_type = "auto", method.ode = "lsoda", - method.modFit = c("Marq", "Port", "SANN", "Nelder-Mead", "BFSG", "CG", "L-BFGS-B"), + method.modFit = c("Port", "Marq", "SANN", "Nelder-Mead", "BFSG", "CG", "L-BFGS-B"), maxit.modFit = "auto", control.modFit = list(), transform_rates = TRUE, @@ -107,13 +103,17 @@ mkinfit(mkinmod, observed, "lsoda" is performant, but sometimes fails to converge. } \item{method.modFit}{ - The optimisation method passed to \code{\link{modFit}}. The default "Marq" - is the Levenberg Marquardt algorithm \code{\link{nls.lm}} from the package - \code{minpack.lm} and usually needs the least number of iterations. + The optimisation method passed to \code{\link{modFit}}. - For more complex problems where local minima occur, the "Port" algorithm is - recommended as it is less prone to get trapped in local minima and depends - less on starting values for parameters. However, it needs more iterations. + In order to optimally deal with problems where local minima occur, the + "Port" algorithm is now used per default as it is less prone to get trapped + in local minima and depends less on starting values for parameters than + the Levenberg Marquardt variant selected by "Marq". However, "Port" needs + more iterations. + + The former default "Marq" is the Levenberg Marquardt algorithm + \code{\link{nls.lm}} from the package \code{minpack.lm} and usually needs + the least number of iterations. The "Pseudo" algorithm is not included because it needs finite parameter bounds which are currently not supported. |