diff options
Diffstat (limited to 'man/mkinfit.Rd')
| -rw-r--r-- | man/mkinfit.Rd | 58 |
1 files changed, 29 insertions, 29 deletions
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index db2f7fda..f2df212f 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -5,11 +5,11 @@ } \description{ This function uses the Flexible Modelling Environment package - \code{\link{FME}} to create a function calculating the model cost, i.e. the + \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 Port algorithm \code{\link{nlminb}}, + 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 + Per default, parameters in the kinetic models are internally transformed in order to better satisfy the assumption of a normal distribution of their estimators. In each step of the optimsation, the kinetic model is solved using the function \code{\link{mkinpredict}}. The variance of the residuals for each @@ -17,10 +17,10 @@ using the argument \code{reweight.method = "obs"}. } \usage{ -mkinfit(mkinmod, observed, +mkinfit(mkinmod, observed, parms.ini = "auto", state.ini = "auto", - fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1], + fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1], from_max_mean = FALSE, solution_type = c("auto", "analytical", "eigen", "deSolve"), method.ode = "lsoda", @@ -30,9 +30,9 @@ mkinfit(mkinmod, observed, control.modFit = list(), transform_rates = TRUE, transform_fractions = TRUE, - plot = FALSE, quiet = FALSE, err = NULL, weight = "none", - scaleVar = FALSE, - atol = 1e-8, rtol = 1e-10, n.outtimes = 100, + plot = FALSE, quiet = FALSE, err = NULL, weight = "none", + scaleVar = FALSE, + atol = 1e-8, rtol = 1e-10, n.outtimes = 100, reweight.method = NULL, reweight.tol = 1e-8, reweight.max.iter = 10, trace_parms = FALSE, ...) @@ -112,12 +112,12 @@ mkinfit(mkinmod, observed, "lsoda" is performant, but sometimes fails to converge. } \item{use_compiled}{ - If set to \code{FALSE}, no compiled version of the \code{\link{mkinmod}} + 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. + a compiled verion is present. } \item{method.modFit}{ - The optimisation method passed to \code{\link{modFit}}. + The optimisation method passed to \code{\link{modFit}}. 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 @@ -138,18 +138,18 @@ mkinfit(mkinmod, observed, } \item{maxit.modFit}{ Maximum number of iterations in the optimisation. If not "auto", this will - be passed to the method called by \code{\link{modFit}}, overriding + be passed to the method called by \code{\link{modFit}}, overriding what may be specified in the next argument \code{control.modFit}. } \item{control.modFit}{ Additional arguments passed to the optimisation method used by - \code{\link{modFit}}. + \code{\link{modFit}}. } \item{transform_rates}{ Boolean specifying if kinetic rate constants should be transformed in the model specification used in the fitting for better compliance with the - assumption of normal distribution of the estimator. If TRUE, also - alpha and beta parameters of the FOMC model are log-transformed, as well + assumption of normal distribution of the estimator. If TRUE, also + alpha and beta parameters of the FOMC model are log-transformed, as well as k1 and k2 rate constants for the DFOP and HS models and the break point tb of the HS model. If FALSE, zero is used as a lower bound for the rates in the optimisation. @@ -157,7 +157,7 @@ mkinfit(mkinmod, observed, \item{transform_fractions}{ Boolean specifying if formation fractions constants should be transformed in the model specification used in the fitting for better compliance with the - assumption of normal distribution of the estimator. The default (TRUE) is + assumption of normal distribution of the estimator. The default (TRUE) is to do transformations. If TRUE, the g parameter of the DFOP and HS models are also transformed, as they can also be seen as compositional data. The transformation used for these transformations is the @@ -193,16 +193,16 @@ mkinfit(mkinmod, observed, \item{n.outtimes}{ The length of the dataseries that is produced by the model prediction function \code{\link{mkinpredict}}. This impacts the accuracy of - the numerical solver if that is used (see \code{solution_type} argument. + the numerical solver if that is used (see \code{solution_type} argument. The default value is 100. } \item{reweight.method}{ The method used for iteratively reweighting residuals, also known as iteratively reweighted least squares (IRLS). Default is NULL, the other method implemented is called "obs", meaning that each - observed variable is assumed to have its own variance, this is + observed variable is assumed to have its own variance, this is estimated from the fit and used for weighting the residuals - in each iteration until convergence of this estimate up to + in each iteration until convergence of this estimate up to \code{reweight.tol} or up to the maximum number of iterations specified by \code{reweight.max.iter}. } @@ -217,19 +217,19 @@ mkinfit(mkinmod, observed, Should a trace of the parameter values be listed? } \item{\dots}{ - Further arguments that will be passed to \code{\link{modFit}}. + Further arguments that will be passed to \code{\link{modFit}}. } } \value{ - A list with "mkinfit" and "modFit" in the class attribute. - A summary can be obtained by \code{\link{summary.mkinfit}}. + A list with "mkinfit" and "modFit" in the class attribute. + A summary can be obtained by \code{\link{summary.mkinfit}}. } \seealso{ Plotting methods \code{\link{plot.mkinfit}} and - \code{\link{mkinparplot}}. + \code{\link{mkinparplot}}. - Fitting of several models to several datasets in a single call to - \code{\link{mmkin}}. + Fitting of several models to several datasets in a single call to + \code{\link{mmkin}}. } \note{ The implementation of iteratively reweighted least squares is inspired by the @@ -238,7 +238,7 @@ mkinfit(mkinmod, observed, other GUI derivative of mkin, sponsored by Syngenta. } \note{ - When using the "IORE" submodel for metabolites, fitting with + When using the "IORE" submodel for metabolites, fitting with "transform_rates = TRUE" (the default) often leads to failures of the numerical ODE solver. In this situation it may help to switch off the internal rate transformation. @@ -257,13 +257,13 @@ SFO_SFO <- mkinmod( parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) # Fit the model to the FOCUS example dataset D using defaults -print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D, +print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = TRUE))) coef(fit) endpoints(fit) \dontrun{ # deSolve is slower when no C compiler (gcc) was available during model generation -print(system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D, +print(system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve"))) coef(fit.deSolve) endpoints(fit.deSolve) @@ -278,7 +278,7 @@ FOMC_SFO <- mkinmod( fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D) # Use starting parameters from parent only FOMC fit fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, plot=TRUE) -fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, +fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, parms.ini = fit.FOMC$bparms.ode, plot=TRUE) # Use stepwise fitting, using optimised parameters from parent only fit, SFORB |