Feature-complete version of the new drfit package that can make use

of the drc package in order to obtain confidence intervals for EDx values.

See ChangeLog for details.



git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@98 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc

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+\name{drcfit}
+\alias{drcfit}
+\title{Fit dose-response models using the drc package}
+\description{
+  Fit dose-response relationships to dose-response data and calculate
+  biometric results for (eco)toxicity evaluation using the drc package
+}
+\usage{
+  drcfit(data, chooseone = TRUE, probit = TRUE, logit = FALSE,
+  weibull = FALSE, linlogit = FALSE, level = 0.95, 
+  showED50 = FALSE, EDx = NULL)
+}
+\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{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.
+    Note that the parameter definitions used in the model are different to the
+    ones used in \code{\link{drfit}}. Parameter e from \code{\link{LN.2}} is listed
+    as a here, and parameter b from LN.2 is listed as b.}
+  \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.
+    Again the parameter definitions used in the model are different to the
+    ones used in \code{\link{drfit}}. Parameter e from \code{\link{LL.2}} is listed
+    as a here, and parameter b from LL.2 is listed as b.}
+  \item{weibull}{
+    A boolean defining if Weibull dose-response models
+    (\code{\link{W1.2}} are fitted to the untransformed dose. Default is FALSE.
+    Note that the results differ from the ones obtained with
+    \code{\link{drfit}}, due to a different model specification.}
+  \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. Obtaining the ED50 (and EDx values
+    in general) uses \code{\link{ED}} internally and does not always give a
+    result.
+  }
+  \item{level}{
+    The level for the confidence interval listed for the log ED50.}
+  \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{EDx}{
+    A vector of inhibition values x in percent for which the corresponding doses
+    EDx should be reported.
+  }
+  \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.
+  }
+}
+\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.
+ 
+    If the parameter \code{showED50} was set to TRUE, the ED50 values and their
+    confidence intervals are also included on the original dose scale.
+
+    If one or more response leves were specified in the argument \code{EDx},
+    the corresponding dose levels are given, together with their confidence
+    intervals.
+  }
+}
+\examples{
+data(antifoul)
+r <- drcfit(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)}} 
+\seealso{
+  Further examples are given in help pages to the datasets
+  \code{\link{antifoul}}, \code{\link{IM1xIPC81}} and
+  \code{\link{IM1xVibrio}}.
+}
+\author{
+  Johannes Ranke 
+  \email{jranke@uni-bremen.de} 
+  \url{http://www.uft.uni-bremen.de/chemie/ranke}
+}
+\keyword{models}
+\keyword{regression}
+\keyword{nonlinear}