Use roxygen for functions and methods

1 files changed, 77 insertions, 75 deletions

diff --git a/man/summary.mkinfit.Rd b/man/summary.mkinfit.Rd
index cbc9098c..fcc1295f 100644
--- a/man/summary.mkinfit.Rd
+++ b/man/summary.mkinfit.Rd
@@ -1,75 +1,77 @@
-\name{summary.mkinfit}

-\alias{summary.mkinfit}

-\alias{print.summary.mkinfit}

-\title{

-  Summary method for class "mkinfit"

-}

-\description{

-  Lists model equations, initial parameter values, optimised parameters with some

-  uncertainty statistics, the chi2 error levels calculated according to FOCUS

-  guidance (2006) as defined therein, formation fractions, DT50 values and

-  optionally the data, consisting of observed, predicted and residual values.

-}

-\usage{

-\method{summary}{mkinfit}(object, data = TRUE, distimes = TRUE, alpha = 0.05, ...)

-\method{print}{summary.mkinfit}(x, digits = max(3, getOption("digits") - 3), ...)

-}

-

-\arguments{

-  \item{object}{

-  an object of class \code{\link{mkinfit}}.

-}

-  \item{x}{

-  an object of class \code{summary.mkinfit}.

-}

-  \item{data}{

-  logical, indicating whether the data should be included in the summary.

-}

-  \item{distimes}{

-  logical, indicating whether DT50 and DT90 values should be included.

-}

-  \item{alpha}{

-  error level for confidence interval estimation from t distribution

-}

-  \item{digits}{

-  Number of digits to use for printing

-}

-  \item{\dots}{

-  optional arguments passed to methods like \code{print}.

-}

-}

-\value{

-  The summary function returns a list with components, among others

-  \item{version, Rversion}{The mkin and R versions used}

-  \item{date.fit, date.summary}{The dates where the fit and the summary were produced}

-  \item{use_of_ff}{Was maximum or minimum use made of formation fractions}

-  \item{residuals, residualVariance, sigma, modVariance, df}{As in summary.modFit}

-  \item{cov.unscaled, cov.scaled, info, niter, stopmess, par}{As in summary.modFit}

-  \item{bpar}{Optimised and backtransformed parameters}

-  \item{diffs }{The differential equations used in the model}

-  \item{data }{The data (see Description above).}

-  \item{start }{The starting values and bounds, if applicable, for optimised parameters.}

-  \item{fixed }{The values of fixed parameters.}

-  \item{errmin }{The chi2 error levels for each observed variable.}

-  \item{bparms.ode }{All backtransformed ODE parameters, for use as starting parameters for

-    related models.}

-  \item{errparms }{Error model parameters. }

-  \item{ff }{The estimated formation fractions derived from the fitted model.}

-  \item{distimes }{The DT50 and DT90 values for each observed variable.}

-  \item{SFORB}{If applicable, eigenvalues of SFORB components of the model.}

-  The print method is called for its side effect, i.e. printing the summary.

-}

-\references{

-  FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and

-  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU

-  Registration} Report of the FOCUS Work Group on Degradation Kinetics,

-  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,

-  \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}

-}

-\author{

-  Johannes Ranke

-}

-\examples{

-  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))

-}

-\keyword{ utilities }

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/summary.mkinfit.R
+\name{summary.mkinfit}
+\alias{summary.mkinfit}
+\alias{print.summary.mkinfit}
+\title{Summary method for class "mkinfit"}
+\usage{
+\method{summary}{mkinfit}(object, data = TRUE, distimes = TRUE,
+  alpha = 0.05, ...)
+
+\method{print}{summary.mkinfit}(x, digits = max(3, getOption("digits") -
+  3), ...)
+}
+\arguments{
+\item{object}{an object of class \code{\link{mkinfit}}.}
+
+\item{data}{logical, indicating whether the data should be included in the
+summary.}
+
+\item{distimes}{logical, indicating whether DT50 and DT90 values should be
+included.}
+
+\item{alpha}{error level for confidence interval estimation from t
+distribution}
+
+\item{\dots}{optional arguments passed to methods like \code{print}.}
+
+\item{x}{an object of class \code{summary.mkinfit}.}
+
+\item{digits}{Number of digits to use for printing}
+}
+\value{
+The summary function returns a list with components, among others
+  \item{version, Rversion}{The mkin and R versions used}
+  \item{date.fit, date.summary}{The dates where the fit and the summary were
+    produced}
+  \item{diffs}{The differential equations used in the model}
+  \item{use_of_ff}{Was maximum or minimum use made of formation fractions}
+  \item{bpar}{Optimised and backtransformed
+    parameters}
+  \item{data}{The data (see Description above).}
+  \item{start}{The starting values and bounds, if applicable, for optimised
+    parameters.}
+  \item{fixed}{The values of fixed parameters.}
+  \item{errmin }{The chi2 error levels for
+    each observed variable.}
+  \item{bparms.ode}{All backtransformed ODE
+    parameters, for use as starting parameters for related models.}
+  \item{errparms}{Error model parameters.}
+  \item{ff}{The estimated formation fractions derived from the fitted
+     model.}
+  \item{distimes}{The DT50 and DT90 values for each observed variable.}
+  \item{SFORB}{If applicable, eigenvalues of SFORB components of the model.}
+  The print method is called for its side effect, i.e. printing the summary.
+}
+\description{
+Lists model equations, initial parameter values, optimised parameters with
+some uncertainty statistics, the chi2 error levels calculated according to
+FOCUS guidance (2006) as defined therein, formation fractions, DT50 values
+and optionally the data, consisting of observed, predicted and residual
+values.
+}
+\examples{
+
+  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
+
+}
+\references{
+FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence
+  and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+  EU Registration} Report of the FOCUS Work Group on Degradation Kinetics,
+  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
+  \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+}
+\author{
+Johannes Ranke
+}