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-rw-r--r--man/IM1xIPC81.Rd7
-rw-r--r--man/IM1xVibrio.Rd8
-rw-r--r--man/antifoul.Rd13
-rw-r--r--man/drcfit.Rd110
-rw-r--r--man/drfit.Rd8
-rw-r--r--man/drplot.Rd7
6 files changed, 149 insertions, 4 deletions
diff --git a/man/IM1xIPC81.Rd b/man/IM1xIPC81.Rd
index 4f5a1dd..dda0c3b 100644
--- a/man/IM1xIPC81.Rd
+++ b/man/IM1xIPC81.Rd
@@ -21,7 +21,12 @@
the tested organism (name of the cell line).
}
\examples{
- \dontrun{demo(IM1xIPC81)}
+ rIM1xIPC81 <- drfit(IM1xIPC81, linlogit = TRUE, showED50 = TRUE, EDx = 10)
+
+ rIM1xIPC81.drc <- drcfit(IM1xIPC81, linlogit = TRUE, showED50 = TRUE, EDx = 10)
+
+ print(rIM1xIPC81,digits=4)
+ print(rIM1xIPC81.drc,digits=4)
}
\source{
Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J,
diff --git a/man/IM1xVibrio.Rd b/man/IM1xVibrio.Rd
index 5315432..cb0bd48 100644
--- a/man/IM1xVibrio.Rd
+++ b/man/IM1xVibrio.Rd
@@ -19,7 +19,13 @@
regarded valid (\code{ok}).
}
\examples{
- \dontrun{demo(IM1xVibrio)}
+ rIM1xVibrio <- drfit(IM1xVibrio, logit = TRUE, chooseone = FALSE,
+ showED50 = TRUE, EDx = c(10, 20))
+ print(rIM1xVibrio, digits = 4)
+
+ rIM1xVibrio.drc <- drcfit(IM1xVibrio, logit = TRUE, chooseone = FALSE,
+ showED50 = TRUE, EDx = c(10, 20))
+ print(rIM1xVibrio.drc, digits = 4)
}
\source{
Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J, Hoffmann J,
diff --git a/man/antifoul.Rd b/man/antifoul.Rd
index 2aa532e..21ae885 100644
--- a/man/antifoul.Rd
+++ b/man/antifoul.Rd
@@ -15,8 +15,19 @@
database are also present.
}
\examples{
- \dontrun{demo(antifoul)}
+rantifoul.ED50 <- drfit(antifoul,
+ linlogit = TRUE, logit = TRUE, weibull = TRUE,
+ chooseone = FALSE,
+ showED50 = TRUE, EDx = c(10))
+print(rantifoul.ED50, digits = 5)
+
+rantifoul.drc <- drcfit(antifoul,
+ linlogit = TRUE, logit = TRUE, weibull = TRUE,
+ chooseone = FALSE,
+ showED50 = TRUE, EDx = c(10))
+print(rantifoul.drc, digits = 5)
}
+
\source{
\url{http://www.uft.uni-bremen.de/chemie}
}
diff --git a/man/drcfit.Rd b/man/drcfit.Rd
new file mode 100644
index 0000000..2da0418
--- /dev/null
+++ b/man/drcfit.Rd
@@ -0,0 +1,110 @@
+\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}
diff --git a/man/drfit.Rd b/man/drfit.Rd
index 7237404..fe84a91 100644
--- a/man/drfit.Rd
+++ b/man/drfit.Rd
@@ -114,6 +114,9 @@
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 in addition.
}
}
\examples{
@@ -123,6 +126,11 @@ 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}
diff --git a/man/drplot.Rd b/man/drplot.Rd
index b2c2745..e9e4dd1 100644
--- a/man/drplot.Rd
+++ b/man/drplot.Rd
@@ -8,7 +8,7 @@
\usage{
drplot(drresults, data, dtype, alpha, ctype, path,
fileprefix, overlay, xlim, ylim, xlab, ylab, axes, frame.plot, postscript,
- pdf, png, bw, pointsize, colors, ltys, devoff, lpos)
+ pdf, png, bw, pointsize, colors, ltys, pchs, devoff, lpos)
}
\arguments{
\item{drresults}{
@@ -99,6 +99,11 @@
\item{ltys}{
This is a vector of line types for the dose-response models, defaulting to 1:8.
}
+ \item{pchs}{
+ This is a vector of character types for the data. The default uses built-in
+ characters 1:n with n being the number of substances for which data are plotted
+ for overlays, or always 1 when no overlay plot is generated.
+ }
\item{lpos}{
An optional argument defaulting to "topright" specifying the position
of the legend by being passed to the legend function. See the help for the

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