diff options
Diffstat (limited to 'man/transform_odeparms.Rd')
-rw-r--r-- | man/transform_odeparms.Rd | 110 |
1 files changed, 57 insertions, 53 deletions
diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd index 006897d6..5c8c90ba 100644 --- a/man/transform_odeparms.Rd +++ b/man/transform_odeparms.Rd @@ -1,66 +1,67 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/transform_odeparms.R \name{transform_odeparms} \alias{transform_odeparms} \alias{backtransform_odeparms} -\title{ - Functions to transform and backtransform kinetic parameters for fitting -} -\description{ - The transformations are intended to map parameters that should only take - on restricted values to the full scale of real numbers. For kinetic rate - constants and other paramters that can only take on positive values, a - simple log transformation is used. For compositional parameters, such as - the formations fractions that should always sum up to 1 and can not be - negative, the \code{\link{ilr}} transformation is used. - - The transformation of sets of formation fractions is fragile, as it supposes - the same ordering of the components in forward and backward transformation. - This is no problem for the internal use in \code{\link{mkinfit}}. -} +\title{Functions to transform and backtransform kinetic parameters for fitting} \usage{ -transform_odeparms(parms, mkinmod, - transform_rates = TRUE, transform_fractions = TRUE) -backtransform_odeparms(transparms, mkinmod, - transform_rates = TRUE, transform_fractions = TRUE) +transform_odeparms(parms, mkinmod, transform_rates = TRUE, + transform_fractions = TRUE) + +backtransform_odeparms(transparms, mkinmod, transform_rates = TRUE, + transform_fractions = TRUE) } \arguments{ - \item{parms}{ - Parameters of kinetic models as used in the differential equations. - } - \item{transparms}{ - Transformed parameters of kinetic models as used in the fitting procedure. - } - \item{mkinmod}{ - The kinetic model of class \code{\link{mkinmod}}, containing the names of - the model variables that are needed for grouping the formation fractions - before \code{\link{ilr}} transformation, the parameter names and - the information if the pathway to sink is included in the model. - } - \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 - as k1 and k2 rate constants for the DFOP and HS models and the break point tb - of the HS model. - } - \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 - to do transformations. 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 \code{\link{ilr}} - transformation. - } +\item{parms}{Parameters of kinetic models as used in the differential +equations.} + +\item{mkinmod}{The kinetic model of class \code{\link{mkinmod}}, containing +the names of the model variables that are needed for grouping the +formation fractions before \code{\link{ilr}} transformation, the parameter +names and the information if the pathway to sink is included in the model.} + +\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 as k1 and k2 rate constants for the DFOP and HS +models and the break point tb of the HS model.} + +\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 to do transformations. 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 \code{\link{ilr}} transformation.} + +\item{transparms}{Transformed parameters of kinetic models as used in the +fitting procedure.} } \value{ - A vector of transformed or backtransformed parameters with the same names - as the original parameters. +A vector of transformed or backtransformed parameters with the same + names as the original parameters. } -\author{ - Johannes Ranke +\description{ +The transformations are intended to map parameters that should only take on +restricted values to the full scale of real numbers. For kinetic rate +constants and other paramters that can only take on positive values, a +simple log transformation is used. For compositional parameters, such as the +formations fractions that should always sum up to 1 and can not be negative, +the \code{\link{ilr}} transformation is used. } +\details{ +The transformation of sets of formation fractions is fragile, as it supposes +the same ordering of the components in forward and backward transformation. +This is no problem for the internal use in \code{\link{mkinfit}}. +} +\section{Functions}{ +\itemize{ +\item \code{backtransform_odeparms}: Backtransform the set of transformed parameters +}} + \examples{ + SFO_SFO <- mkinmod( parent = list(type = "SFO", to = "m1", sink = TRUE), m1 = list(type = "SFO")) @@ -113,5 +114,8 @@ fit.ff.2.s <- summary(fit.ff.2) print(fit.ff.2.s$par, 3) print(fit.ff.2.s$bpar, 3) } + +} +\author{ +Johannes Ranke } -\keyword{ manip } |