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-rw-r--r--man/mkinfit.Rd24
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.

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