Fork the gmkin GUI from mkin. See ChangeLog for details

1 files changed, 0 insertions, 69 deletions

diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd
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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 }