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-rw-r--r--man/drfit.Rd84
-rw-r--r--man/drplot.Rd5
-rwxr-xr-x[-rw-r--r--]man/linlogitf.Rd (renamed from man/linearlogisf.Rd)6
3 files changed, 60 insertions, 35 deletions
diff --git a/man/drfit.Rd b/man/drfit.Rd
index 2ec4a73..0d9ee6f 100644
--- a/man/drfit.Rd
+++ b/man/drfit.Rd
@@ -6,58 +6,84 @@
biometric results for (eco)toxicity evaluation
}
\usage{
- drfit(data, startlogEC50 = NA, chooseone = TRUE, lognorm = TRUE, logis = FALSE,
- linearlogis = FALSE, linearlogisWrong = NA, allWrong = NA, b0 = 2, f0 = 0)
+ drfit(data, startlogEC50 = NA, chooseone = TRUE, probit = TRUE, logit = FALSE,
+ weibull = FALSE, linlogit = FALSE, linlogitWrong = NA, allWrong = NA,
+ b0 = 2, f0 = 0)
}
\arguments{
\item{data}{
- A data frame as returned from \code{\link{drdata}}. The data frame has to
+ A data frame containing dose-response data. The data frame has to
contain at least a factor called "substance", a vector called "unit"
containing the unit used for the dose, a column "response" with the
response values of the test system normalized between 0 and 1 and a column
- "dose" with the numeric dose values. For later use of the
- \code{\link{drplot}} function, a factor called "dosefactor" also has to be
- present, containing the dose as a factor. If there is a column called "ok"
- and it is set to "no fit", then the corresponding data point will be excluded
- from the fitting procedure.
+ "dose" with the numeric dose values. 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 "ok" and it is set to "no fit" in a specific
+ line, then the corresponding data point will be excluded from the fitting
+ procedure, although it will be plotted.
}
\item{startlogEC50}{
- Especially for the linearlogis model, a suitable log10 of the EC50 has to be given
+ Especially for the linlogit model, a suitable log10 of the EC50 has to be given
by the user, since it is not correctly estimated for data showing hormesis with
the default estimation method.}
- \item{lognorm}{
+ \item{probit}{
A boolean defining if cumulative density curves of normal distributions
- are fitted to the data. Default ist TRUE.}
- \item{logis}{
- A boolean defining if cumulative densitiy curves of logistic distributions
- are fitted to the data. Default is FALSE.}
- \item{linearlogis}{
+ \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{linearlogisf}} as defined by van Ewijk and Hoekstra 1993 is
+ \code{\link{linlogitf}} as defined by van Ewijk and Hoekstra 1993 is
fitted to the data. Default is FALSE.}
- \item{linearlogisWrong}{
+ \item{linlogitWrong}{
An optional vector containing the names of the substances for which the
- linearlogis function produces a wrong fit.}
+ linlogit function produces a wrong fit.}
\item{allWrong}{
An optional vector containing the names of the substances for which all
- functions produces a wrong fit.}
+ functions produce a wrong fit.}
\item{chooseone}{
- If TRUE (default), the models are tried in the order linearlogis, logis and lognorm,
- and the first model that produces a valid fit is used. Usually this will be the one
- with the lowest residual standard deviation. If FALSE, all models that are set to TRUE
- and that can be fitted will be reported.}
+ If TRUE (default), the models are tried in the order linlogit, weibull,
+ logit, probit, 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{b0,f0}{
If the linearlogistic model is fitted, b0 and f0 give the possibility to
adapt the starting values for the parameters b and f.}
}
\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 "none".
- Every successful fit is reported in one line. Parameters of the fitted curves are only
- reported if the fitted EC50 is not higher than the highest dose.}
-
-}
+ 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 "none".
+ Every successful fit is reported in one line. Parameters of the fitted
+ curves are only reported if the fitted EC50 is not higher than the
+ highest dose.
+ \code{n} is the number of dose-response curves in the raw data (repetitions
+ in each point), \code{lld} is the decadic logarithm of the lowest dose and
+ \code{lhd} is the decadic logarithm of the highest dose.
+ For the "linlogit", "logit" and "probit" models, the parameter
+ \code{a} that is reported coincides with the logEC50, i.e the logEC50 is
+ one of the model parameters that is being fitted, and therefore
+ a standard deviation \code{std} is reported for the logEC50. In the
+ case of the "weibull" model, \code{a} is a location parameter.
+ Parameter \code{b} in the case of the "linlogit" fit is the variable
+ b from the \code{\link{linlogitf}} function. In the case of "probit" fit
+ it is the standard deviation of the fitted normal distribution, in the case
+ of the "logit" fit it is the \code{scale} parameter in the \code{\link{plogis}}
+ function, and in the "weibull" fit it is the \code{shape} parameter of the
+ fitted \code{\link{pweibull}} function. Only the "linlogit" fit produces a
+ third parameter \code{c} which is the variable f from the
+ \code{\link{linlogitf}} function.}
+ }
\examples{
data(antifoul)
r <- drfit(antifoul)
diff --git a/man/drplot.Rd b/man/drplot.Rd
index ecd6895..e5201a2 100644
--- a/man/drplot.Rd
+++ b/man/drplot.Rd
@@ -80,9 +80,8 @@
}
\note{
- Treatment of legends is not really well solved. Be sure all devices are
- closed (e.g. by calling \code{dev.off()}) before calling \code{drplot}
- again after a failure.
+ Be sure all devices are closed (e.g. by calling \code{dev.off()}) before
+ calling \code{drplot} again after a failure.
}
\examples{
data(antifoul)
diff --git a/man/linearlogisf.Rd b/man/linlogitf.Rd
index 1ebe8be..2eca8c4 100644..100755
--- a/man/linearlogisf.Rd
+++ b/man/linlogitf.Rd
@@ -1,12 +1,12 @@
-\name{linearlogisf}
-\alias{linearlogisf}
+\name{linlogitf}
+\alias{linlogitf}
\title{Linear-logistic function}
\description{
Helper function describing a special type of dose-response curves, showing a stimulus
at subtoxic doses.
}
\usage{
- linearlogisf(x,k,f,mu,b)
+ linlogitf(x,k,f,mu,b)
}
\arguments{
\item{x}{

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