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\name{drfit}
\alias{drfit}
\title{Fit dose-response models}
\description{
Fit dose-response relationships to dose-response data and calculate
biometric results for (eco)toxicity evaluation
}
\usage{
drfit(data, startlogED50 = NA, chooseone = TRUE, probit = TRUE, logit = FALSE,
weibull = FALSE, linlogit = FALSE, level = 0.95, linlogitWrong = NA,
allWrong = NA, ps0 = 1, ls0 = 0.5, ws0 = 0.5, b0 = 2, f0 = 0,
showED50 = FALSE,
EDx = NULL, EDx.tolerance = 1e-4)
}
\arguments{
\item{data}{
A data frame containing dose-response data. The data frame has to contain
at least a factor called \dQuote{substance}, a numeric vector \dQuote{dose}
with the dose values, a vector called \dQuote{unit} containing the unit
used for the dose and a numeric vector \dQuote{response} with the response
values of the test system normalized between 0 and 1. Such a data frame can
be easily obtained if a compliant RODBC data source is available for use in
conjunction with the function \code{\link{drdata}}.
If there is a column called \dQuote{ok} and it is set to \dQuote{no fit} in
a specific line, then the corresponding data point will be excluded from
the fitting procedure, although it will be plotted.}
\item{startlogED50}{
Especially for the linlogit model, a suitable log10 of the ED50 has to be
given by the user, since it is not correctly estimated for data showing
hormesis with the default estimation method.}
\item{probit}{
A boolean defining if cumulative density curves of normal distributions
\code{\link{pnorm}} are fitted against the decadic logarithm of the dose.
Default ist TRUE.}
\item{logit}{
A boolean defining if cumulative density curves of logistic distributions
\code{\link{plogis}} are fitted to the decadic logarithm of the dose.
Default is FALSE.}
\item{weibull}{
A boolean defining if the cumulative density curves of weibull distributions
(\code{\link{pweibull}} with additionall location parameter and scale=1)
are fitted to the decadic logarithm of the dose. Default is FALSE.}
\item{linlogit}{
A boolean defining if the linear-logistic function
\code{\link{linlogitf}} as defined by van Ewijk and Hoekstra 1993 is
fitted to the data. Default is FALSE.}
\item{level}{
The level for the confidence interval listed for the log ED50.}
\item{linlogitWrong}{
An optional vector containing the names of the substances for which the
linlogit function produces a wrong fit.}
\item{allWrong}{
An optional vector containing the names of the substances for which all
functions produce a wrong fit.}
\item{chooseone}{
If TRUE (default), the models are tried in the order linlogit, probit,
logit, weibull, and the first model that produces a valid fit is used.
If FALSE, all models that are set to TRUE and that can be fitted will be
reported.}
\item{ps0}{
If the probit model is fitted, \code{ps0} gives the possibility to adjust
the starting value for the scale parameter of \code{\link{pnorm}}.}
\item{ls0}{
If the logit model is fitted, \code{ls0} gives the possibility to adjust
the starting value for the scale parameter of \code{\link{plogis}}.}
\item{ws0}{
If the weibull model is fitted, \code{ws0} gives the possibility to adjust
the starting value for the shape parameter of \code{\link{pweibull}}.}
\item{b0,f0}{
If the linearlogistic model is fitted, \code{b0} and \code{f0} give the
possibility to adjust the starting values for the parameters b and f.}
\item{showED50}{
If set to TRUE, the ED50 and its confidence interval on the original dose
scale (not log scale) is included in the output.
}
\item{EDx}{
A vector of inhibition values x in percent for which the corresponding doses
EDx should be reported.
}
\item{EDx.tolerance}{
Tolerance of the effect level, expressed on the response scale from 0 to 1.
}
}
\value{
\item{results}{
A data frame containing at least one line for each substance. If the data
did not show a mean response < 0.5 at the highest dose level, the
modeltype is set to \dQuote{inactive}. If the mean response at the lowest
dose is smaller than 0.5, the modeltype is set to \dQuote{active}. In
both cases, no fitting procedure is carried out. Every successful fit is
reported in one line. Parameters of the fitted curves are only reported
if the fitted ED50 is not higher than the highest dose.
\code{ndl} is the number of dose levels in the raw data, \code{n} is the
total number of data points in the raw data used for the fit
\code{lld} is the decadic logarithm of the lowest dose and
\code{lhd} is the decadic logarithm of the highest dose. For the
\dQuote{linlogit}, \dQuote{logit} and \dQuote{probit} models, the
parameter \code{a} that is reported coincides with the logED50, i.e the
logED50 is one of the model parameters that is being fitted. Therefore,
a confidence interval for the confidence level \code{level} is calculated
using the \code{\link[MASS:confint]{confint.nls}} function and listed.
In the case of the \dQuote{weibull} model, \code{a} is a
location parameter. Parameter \code{b} in the case of the
\dQuote{linlogit} fit is the variable b from the \code{\link{linlogitf}}
function. In the case of \dQuote{probit} fit it is the standard deviation
of the fitted normal distribution, in the case of the \dQuote{logit} fit
it is the \code{scale} parameter in the \code{\link{plogis}} function,
and in the \dQuote{weibull} fit it is the \code{shape} parameter of the
fitted \code{\link{pweibull}} function. Only the \dQuote{linlogit} fit
produces a third parameter \code{c} which is the variable f from the
\code{\link{linlogitf}} function.
If the parameter \code{showED50} was set to TRUE, the ED50 values and their
confidence intervals are also included on the original dose scale.
}
}
\examples{
data(antifoul)
r <- drfit(antifoul, showED50 = TRUE, EDx = c(5, 10, 20))
format(r, digits = 2)
}
\note{There is a demo for each dataset that can be accessed by
\code{demo(dataset)}}
\author{
Johannes Ranke
\email{jranke@uni-bremen.de}
\url{http://www.uft.uni-bremen.de/chemie/ranke}
}
\keyword{models}
\keyword{regression}
\keyword{nonlinear}
|
