Added the drfit-package help page, a new sample data file

and a preliminary version of the drfit-Rnews article.

R/drfit.R
- the possibility to directly write pdf graphs was added
- the results dataframe now has numbered lines where it didn't

The checkplate and checksubstance functions are now classified
internal in their help files.



git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@57 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc

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