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authorranke <ranke@d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc>2006-04-26 14:17:35 +0000
committerranke <ranke@d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc>2006-04-26 14:17:35 +0000
commitec7b765978d3d54739d9c8de905eac743c68b613 (patch)
tree5961038ee34c8ecfdc1bb084a531212aaf86fb70
parent0dbb88867fbcdfbcee73beb8a971b10ab80da3d1 (diff)
Took out tabs from R help files, and fixed the formatting.
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@71 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
-rw-r--r--man/IM1xIPC81.Rd20
-rw-r--r--man/IM1xVibrio.Rd21
-rw-r--r--man/checkexperiment.Rd6
-rw-r--r--man/drfit.Rd94
-rw-r--r--man/drplot.Rd19
-rw-r--r--man/pyrithione.Rd4
6 files changed, 82 insertions, 82 deletions
diff --git a/man/IM1xIPC81.Rd b/man/IM1xIPC81.Rd
index 093f142..40aaa81 100644
--- a/man/IM1xIPC81.Rd
+++ b/man/IM1xIPC81.Rd
@@ -3,16 +3,16 @@
\alias{IM1xIPC81}
\title{Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells}
\description{
- This is the raw data documenting the influence of the alkyl
- chain length in 3 position on the toxicity to the
- promyelocytic leukemia rat cell line IPC-81. The substances
- are named according to the UFT naming scheme of these
- substances. IM13 BF4 means 1-methyl-3-propylimidazolium
- tetrafluoroborate, IM14 BF4 means
- 1-methyl-3-butylimidazolium tetrafluoroborate and IM1-10
- BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate.
- This is a subset (only the BF4 anion) of the data
- shown in Figure 3 in Ranke et al. (2004).
+ This is the raw data documenting the influence of the alkyl
+ chain length in 3 position on the toxicity to the
+ promyelocytic leukemia rat cell line IPC-81. The substances
+ are named according to the UFT naming scheme of these
+ substances. IM13 BF4 means 1-methyl-3-propylimidazolium
+ tetrafluoroborate, IM14 BF4 means
+ 1-methyl-3-butylimidazolium tetrafluoroborate and IM1-10
+ BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate.
+ This is a subset (only the BF4 anion) of the data
+ shown in Figure 3 in Ranke et al. (2004).
}
\usage{data(IM1xIPC81)}
\format{
diff --git a/man/IM1xVibrio.Rd b/man/IM1xVibrio.Rd
index 79936d6..454e099 100644
--- a/man/IM1xVibrio.Rd
+++ b/man/IM1xVibrio.Rd
@@ -3,19 +3,20 @@
\alias{IM1xVibrio}
\title{Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri}
\description{
- This is the raw data documenting the influence of the alkyl chain length in 3 position
- on the toxicity to the marine luminescent bacteria \emph{V. fischeri}. The substances
- are named according to the UFT naming scheme of these substances. IM13 BF4
- means 1-methyl-3-propylimidazolium tetrafluoroborate, IM14 BF4 means
- 1-methyl-3-butylimidazolium tetrafluoroborate and IM1-10 BF4 means
- 1-methyl-3-decylimidazolium tetrafluoroborate.
+ This is the raw data documenting the influence of the alkyl chain length in 3
+ position on the toxicity to the marine luminescent bacteria \emph{V.
+ fischeri}. The substances are named according to the UFT naming scheme of
+ these substances.
+ IM13 BF4 means 1-methyl-3-propylimidazolium tetrafluoroborate,
+ IM14 BF4 means 1-methyl-3-butylimidazolium tetrafluoroborate and
+ IM1-10 BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate.
}
\usage{data(IM1xVibrio)}
\format{
- A dataframe containing the data as required for the \code{\link{drfit}} function. Additional
- columns contain the species tested (luminescent bacteria Vibrio fischeri, \code{organism}),
- and a field specifying if the data is regarded valid
- (\code{ok}).
+ A dataframe containing the data as required for the \code{\link{drfit}}
+ function. Additional columns contain the species tested (luminescent bacteria
+ Vibrio fischeri, \code{organism}), and a field specifying if the data is
+ regarded valid (\code{ok}).
}
\source{
Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J, Hoffmann J,
diff --git a/man/checkexperiment.Rd b/man/checkexperiment.Rd
index 54352e8..d68cd87 100644
--- a/man/checkexperiment.Rd
+++ b/man/checkexperiment.Rd
@@ -14,9 +14,9 @@
\item{id}{
The id of the experiment or the plate identifying it within the database.}
\item{db}{
- The database to be used. Currently, the microtiter plate databases
- "cytotox", "enzymes" of the UFT Department of Bioorganic Chemistry are
- supported, as well as the database of ecotoxicity experiments "ecotox".}
+ The database to be used. Currently, the microtiter plate databases
+ "cytotox", "enzymes" of the UFT Department of Bioorganic Chemistry are
+ supported, as well as the database of ecotoxicity experiments "ecotox".}
}
\value{
The function lists a report and shows two graphs side by side.
diff --git a/man/drfit.Rd b/man/drfit.Rd
index fefea85..9eb5476 100644
--- a/man/drfit.Rd
+++ b/man/drfit.Rd
@@ -2,31 +2,31 @@
\alias{drfit}
\title{Fit dose-response models}
\description{
- Fit dose-response relationships to dose-response data and calculate
+ Fit dose-response relationships to dose-response data and calculate
biometric results for (eco)toxicity evaluation
}
\usage{
drfit(data, startlogED50 = NA, chooseone = TRUE, probit = TRUE, logit = FALSE,
- weibull = FALSE, linlogit = FALSE, conf = FALSE, linlogitWrong = NA,
- allWrong = NA, s0 = 0.5, b0 = 2, f0 = 0)
+ weibull = FALSE, linlogit = FALSE, conf = FALSE, linlogitWrong = NA,
+ allWrong = NA, s0 = 0.5, b0 = 2, f0 = 0)
}
\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.}
+ 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{startlogED50}{
- Especially for the linlogit model, a suitable log10 of the ED50 has to be given
- by the user, since it is not correctly estimated for data showing hormesis with
- the default estimation method.}
+ Especially for the linlogit model, a suitable log10 of the ED50 has to be
+ given by the user, since it is not correctly estimated for data showing
+ hormesis with the default estimation method.}
\item{probit}{
A boolean defining if cumulative density curves of normal distributions
\code{\link{pnorm}} are fitted against the decadic logarithm of the dose.
@@ -44,9 +44,9 @@
\code{\link{linlogitf}} as defined by van Ewijk and Hoekstra 1993 is
fitted to the data. Default is FALSE.}
\item{conf}{
- A boolean defining if a confidence interval of the log ED50 is to be
- listed for alpha = 5 \% (two-sided). If FALSE (default), the standard
- deviation is listed in the output of drfit.}
+ A boolean defining if a confidence interval of the log ED50 is to be
+ listed for alpha = 5 \% (two-sided). If FALSE (default), the standard
+ deviation is listed in the output of drfit.}
\item{linlogitWrong}{
An optional vector containing the names of the substances for which the
linlogit function produces a wrong fit.}
@@ -67,34 +67,34 @@
}
\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 \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.
+ 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. 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, depending on the argument \code{conf}, a standard deviation
- \code{std} or a confidence interval \code{conf} 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.}
-}
+ \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. 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, depending on the argument \code{conf}, a standard deviation
+ \code{std} or a confidence interval \code{conf} 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 2f1d4ae..f8f8aa8 100644
--- a/man/drplot.Rd
+++ b/man/drplot.Rd
@@ -2,7 +2,7 @@
\alias{drplot}
\title{Plot dose-response models}
\description{
- Produce graphics of dose-response data and dose-response relationships
+ Produce graphics of dose-response data and dose-response relationships
either combined or separately, for one or more substances.
}
\usage{
@@ -34,18 +34,18 @@
}
\item{ctype}{
This argument decides if horizontal lines are drawn to show the scatter of
- the control values (dose = 0), if there are more than three of them.
- Defaults to "none", further allowed values are "std" and "conf" for
- displaying the standard deviation of the controls or the confidence
- interval for the mean of the controls.
+ the control values (dose = 0), if there are more than three of them.
+ Defaults to "none", further allowed values are "std" and "conf" for
+ displaying the standard deviation of the controls or the confidence
+ interval for the mean of the controls.
}
\item{path}{
The path where graphic files should be put if any are produced. Defaults
to "./" i.e. the current working directory of R.
}
\item{fileprefix}{
- A string which will form the beginning of each filename, if graphic files
- are created. Defaults to "drplot".
+ A string which will form the beginning of each filename, if graphic files
+ are created. Defaults to "drplot".
}
\item{overlay}{
If TRUE, all output will be put into one graph, otherwise a separate graph
@@ -71,8 +71,8 @@
}
\item{png}{
If TRUE, (a) png graph(s) will be created. Otherwise, and if the
- postscript and pdf arguments are 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
@@ -99,7 +99,6 @@
You will get plots of data and/or the fitted dose-response curves, on the
screen and/or as postscript files, depending on the parameters.
}
-
}
\note{
Be sure all devices are closed (e.g. by calling \code{dev.off()}) before
diff --git a/man/pyrithione.Rd b/man/pyrithione.Rd
index 4ea72cc..b24a906 100644
--- a/man/pyrithione.Rd
+++ b/man/pyrithione.Rd
@@ -9,8 +9,8 @@
}
\usage{data(pyrithione)}
\format{
- A dataframe containing the data as required for the \code{\link{drfit}} function.
-}
+ A dataframe containing the data as required for the \code{\link{drfit}}
+ function. }
\source{
Doose C, Ranke J, Stock F, Bottin-Weber U, Jastorff B (2004)
Structure-activity relationships of pyrithiones - IPC-81 toxicity tests with

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