Use roxygen for functions and methods

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 }