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authorranke <ranke@d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc>2014-02-25 17:30:01 +0000
committerranke <ranke@d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc>2014-02-25 17:30:01 +0000
commit35362cfc7c02f12fd9689f68a772a804d895535a (patch)
tree7171ac4ee23fa4e56135970936e488b4836e49a8 /man/drcfit.Rd
parent184aacf1ad5a28b2428633cd1966d6fb881eb3b0 (diff)
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}

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