aboutsummaryrefslogtreecommitdiff
path: root/man
diff options
context:
space:
mode:
Diffstat (limited to 'man')
-rw-r--r--man/XY.Rd16
-rw-r--r--man/checkplate.Rd1
-rw-r--r--man/checksubstance.Rd1
-rw-r--r--man/drfit-package.Rd29
-rw-r--r--man/drfit.Rd74
-rw-r--r--man/drplot.Rd11
6 files changed, 93 insertions, 39 deletions
diff --git a/man/XY.Rd b/man/XY.Rd
new file mode 100644
index 0000000..ae28e99
--- /dev/null
+++ b/man/XY.Rd
@@ -0,0 +1,16 @@
+\name{XY}
+\docType{data}
+\alias{XY}
+\title{Dose-Response data for two substances X and Y}
+\description{
+ This is just a sample data set for two substances named X and Y.
+}
+\usage{data(antifoul)}
+\format{
+ A dataframe containing dose (concentration) and response data, as well as
+ control values where the dose is zero.
+}
+\source{
+ \url{http://www.uft.uni-bremen.de/chemie}
+}
+\keyword{datasets}
diff --git a/man/checkplate.Rd b/man/checkplate.Rd
index 39eea85..794b3f6 100644
--- a/man/checkplate.Rd
+++ b/man/checkplate.Rd
@@ -30,3 +30,4 @@
\url{http://www.uft.uni-bremen.de/chemie/ranke}
}
\keyword{database}
+\keyword{internal}
diff --git a/man/checksubstance.Rd b/man/checksubstance.Rd
index 3871a87..59759e8 100644
--- a/man/checksubstance.Rd
+++ b/man/checksubstance.Rd
@@ -43,3 +43,4 @@
\url{http://www.uft.uni-bremen.de/chemie/ranke}
}
\keyword{database}
+\keyword{internal}
diff --git a/man/drfit-package.Rd b/man/drfit-package.Rd
new file mode 100644
index 0000000..ac91a35
--- /dev/null
+++ b/man/drfit-package.Rd
@@ -0,0 +1,29 @@
+\name{drfit-package}
+\alias{drfit-package}
+\docType{package}
+\title{
+Dose-response data evaluation
+}
+\description{
+See \url{../DESCRIPTION}
+}
+\details{
+There is an introductory article located in \url{../doc/drfit-Rnews.pdf}.
+}
+\author{
+Author and Maintainer: Johannes Ranke <jranke@uni-bremen.de>
+}
+\keyword{ package }
+\keyword{ models }
+\keyword{ regression }
+\keyword{ nonlinear }
+\seealso{
+There is another, more sophisticated package with similar functionality
+called \code{\link[drc:drc-package]{drc}
+}
+\examples{
+data(antifoul)
+r <- drfit(antifoul)
+format(r,digits=2)
+\dontrun{drplot(r,antifoul,overlay=TRUE,bw=FALSE)}
+}
diff --git a/man/drfit.Rd b/man/drfit.Rd
index bbe7496..6e9ef47 100644
--- a/man/drfit.Rd
+++ b/man/drfit.Rd
@@ -12,17 +12,17 @@
}
\arguments{
\item{data}{
- A data frame containing dose-response data. The data frame has to
- contain at least a factor called "substance", a numeric vector "dose" with
- the dose values, a vector called "unit" containing the unit used for the
- dose and a numeric vector "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}}.
+ 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 "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.
+ 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
@@ -64,32 +64,34 @@
}
\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 "inactive". If the mean response at the lowest dose
- is smaller than 0.5, the modeltype is set to "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
- rounded mean of the number of replicates at each dose level in the raw
- data, \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 logED50, i.e the logED50 is
- one of the model parameters that is being fitted, and therefore
- a standard deviation \code{std} is reported for the logED50. 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.}
- }
+ 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
+ rounded mean of the number of replicates at each dose level in the raw
+ data, \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, and
+ therefore a standard deviation \code{std} is reported for the logED50. 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.}
+
+}
\examples{
data(antifoul)
r <- drfit(antifoul)
diff --git a/man/drplot.Rd b/man/drplot.Rd
index 99f77ab..09a8517 100644
--- a/man/drplot.Rd
+++ b/man/drplot.Rd
@@ -53,13 +53,18 @@
}
\item{postscript}{
If TRUE, (a) postscript graph(s) will be created. Otherwise, and if
- the png argument is also FALSE, graphics will be
+ the pdf and png arguments are also FALSE, graphics will be
+ displayed with a screen graphics device.
+ }
+ \item{pdf}{
+ If TRUE, (a) pdf graph(s) will be created. Otherwise, and if
+ the postscript and png arguments are also FALSE, graphics will be
displayed with a screen graphics device.
}
\item{png}{
If TRUE, (a) png graph(s) will be created. Otherwise, and if the
- postscript argument is also FALSE, graphics will be displayed with a
- screen graphics device.
+ postscript and pdf arguments are also FALSE, graphics will be displayed
+ with a screen graphics device.
}
\item{bw}{
A boolean deciding if the plots will be black and white or not. Default

Contact - Imprint