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authorJohannes Ranke <jranke@uni-bremen.de>2014-05-07 14:47:28 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2014-05-07 14:47:28 +0200
commite959fde98f95f3595e01490b67892678bbcd1b27 (patch)
tree992c56223a31c6937091dd5f9eeef63c2dd9e579 /man/transform_odeparms.Rd
parentd846ac7691ab648afbb5a98bbca91911396a95bf (diff)
Fork the gmkin GUI from mkin. See ChangeLog for details
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-\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.
-}
-\usage{
-transform_odeparms(parms, mod_vars, transform_rates = TRUE, transform_fractions = TRUE)
-backtransform_odeparms(transparms, mod_vars,
- 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{mod_vars}{
- Names of the state variables in the kinetic model. These are used for
- grouping the formation fractions before \code{\link{ilr}} transformation.
- }
- \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.
- }
-}
-\value{
- A vector of transformed or backtransformed parameters with the same names
- as the original parameters.
-}
-\author{
- Johannes Ranke
-}
-\examples{
-SFO_SFO <- mkinmod(
- parent = list(type = "SFO", to = "m1", sink = TRUE),
- m1 = list(type = "SFO"))
-# Fit the model to the FOCUS example dataset D using defaults
-fit <- mkinfit(SFO_SFO, FOCUS_2006_D)
-summary(fit, data=FALSE) # See transformed and backtransformed parameters
-initials <- fit$start$value
-transformed <- fit$start$transformed
-names(initials) <- names(transformed) <- rownames(fit$start)
-transform_odeparms(initials, c("parent", "m1"))
-backtransform_odeparms(transformed, c("parent", "m1"))
-}
-\keyword{ manip }

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