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-rw-r--r--man/transform_odeparms.Rd110
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 }

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