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

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