- Fixed the drplot function, so the graphics parameter ask is adequately set

  depending on the overlay argument, and set back to the previous value
- Added a test for each datase
- Added a demo for each dataset
- Corrected many small bugs in the documentation and improved formatting
  of the .Rd files



git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@74 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc

11 files changed, 64 insertions, 45 deletions

diff --git a/man/IM1xIPC81.Rd b/man/IM1xIPC81.Rd
index 40aaa81..4f5a1dd 100644
--- a/man/IM1xIPC81.Rd
+++ b/man/IM1xIPC81.Rd
@@ -20,6 +20,9 @@
   \code{\link{drfit}} function. An additional column contains
   the tested organism (name of the cell line).
 }
+\examples{
+  \dontrun{demo(IM1xIPC81)}
+}
 \source{
   Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J,
   Hoffmann J, Ondruschka B, Filser J, Jastorff B (2004)
diff --git a/man/IM1xVibrio.Rd b/man/IM1xVibrio.Rd
index 454e099..5315432 100644
--- a/man/IM1xVibrio.Rd
+++ b/man/IM1xVibrio.Rd
@@ -18,6 +18,9 @@
   Vibrio fischeri, \code{organism}), and a field specifying if the data is
   regarded valid (\code{ok}).
 }
+\examples{
+  \dontrun{demo(IM1xVibrio)}
+}
 \source{
   Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J, Hoffmann J,
   Ondruschka B, Filser J, Jastorff B (2004) Biological effects of imidazolium
diff --git a/man/XY.Rd b/man/XY.Rd
index ab304ba..8022264 100644
--- a/man/XY.Rd
+++ b/man/XY.Rd
@@ -11,6 +11,9 @@
   A dataframe containing dose (concentration) and response data, as well as
   control values where the dose is zero.
 }
+\examples{
+  \dontrun{demo(XY)}
+}
 \source{
   \url{http://www.uft.uni-bremen.de/chemie}
 }
diff --git a/man/antifoul.Rd b/man/antifoul.Rd
index bebec41..2aa532e 100644
--- a/man/antifoul.Rd
+++ b/man/antifoul.Rd
@@ -14,6 +14,9 @@
   for TBT and Zink Pyrithione, respectively. Some additional columns from the
   database are also present.
 }
+\examples{
+  \dontrun{demo(antifoul)}
+}
 \source{
   \url{http://www.uft.uni-bremen.de/chemie}
 }
diff --git a/man/checkexperiment.Rd b/man/checkexperiment.Rd
index d68cd87..56db90c 100644
--- a/man/checkexperiment.Rd
+++ b/man/checkexperiment.Rd
@@ -22,8 +22,8 @@
   The function lists a report and shows two graphs side by side.
 }
 \examples{
-# Check plate number 1 in the cytotox database
-\dontrun{data <- checkplate(3)}
+# Check plate number 3 in the cytotox database
+\dontrun{checkplate(3)}
 }
 \author{
   Johannes Ranke 
diff --git a/man/checksubstance.Rd b/man/checksubstance.Rd
index 59759e8..f5340fe 100644
--- a/man/checksubstance.Rd
+++ b/man/checksubstance.Rd
@@ -16,13 +16,15 @@
     of the UFT Department of Bioorganic Chemistry are supported (default is
     "cytotox").} 
   \item{experimentator}{
-    The name of the experimentator whose data is to be used. Default is "\%", which
-    means that data from all experimentators are shown.}
+    The name of the experimentator whose data is to be used. Default is "\%",
+    which means that data from all experimentators are shown.}
   \item{celltype}{
-    Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are supported.
-    Default is "\%", i.e. data for any cell type will be displayed.}
+    Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are
+    supported.  Default is "\%", i.e. data for any cell type will be
+    displayed.}
   \item{enzymetype}{
-    Currently, only data for AChE, GR and GST are supported. The default value is "\%", i.e. data for any enzyme type will be displayed.}
+    Currently, only data for AChE, GR and GST are supported. The default value
+    is "\%", i.e. data for any enzyme type will be displayed.}
   \item{whereClause}{
     With this argument, additional conditions for the SQL query can be set, 
     e.g. "where plate != 710". The default is 1 (in SQL syntax this means TRUE).}
diff --git a/man/drdata.Rd b/man/drdata.Rd
index 0c1e901..8f545da 100644
--- a/man/drdata.Rd
+++ b/man/drdata.Rd
@@ -1,8 +1,8 @@
 \name{drdata}
 \alias{drdata}
-\title{Get dose-response data}
+\title{Get dose-response data via RODBC}
 \description{
-	Get dose-response data from a remote mysql server 
+	Get dose-response data from an adequate ODBC data source
 }
 \usage{
   drdata(substances, experimentator = "\%", db = "cytotox", celltype = "IPC-81", 
@@ -14,39 +14,40 @@
     A string or an array of strings with the substance names for
     which dose-response data is to be retrieved.}
   \item{experimentator}{
-    The name of the experimentator whose data is to be used. Default is "%", which
-    means that data from all experimentators are retrieved.}
+    The name of the experimentator whose data is to be used. Default is "%",
+    which means that data from all experimentators are retrieved.}
   \item{db}{
-    The database to be used. Currently, the databases "cytotox" and "enzymes"
-    of the UFT Department of Bioorganic Chemistry are supported (default is
-    "cytotox").} 
+    The database to be used. Currently, the databases "cytotox", "enzymes"
+    and "ecotox" of the UFT Department of Bioorganic Chemistry are 
+    supported (default is "cytotox").} 
   \item{celltype}{
-    Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are supported.}
+    Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are
+    supported.} 
   \item{enzymetype}{
     Currently, only data for AChE, GR and GST are supported.}
   \item{organism}{
     The organism that was exposed to the chemical. Only important if the database
     "ecotox" is used. Defaults to "Vibrio fischeri".}
   \item{endpoint}{
-    The endpoint that should be used for selecting the data. Only important if the
-    database "ecotox" is used. Defaults to "Vibrio fischeri".}
+    The endpoint that should be used for selecting the data. Only important if
+    the database "ecotox" is used. Defaults to "Luminescence".}
   \item{whereClause}{
     With this argument, additional conditions for the SQL query can be set, 
     e.g. "plate != 710" (i.e. "Do not retrieve data for plate 710"). The
     default is 1 (in SQL syntax this means TRUE).} 
   \item{ok}{
-    With the default value "'ok','no fit'", only data that has been checked and set to "ok"
-    or "no fit" in the database is retrieved. The argument "no fit" will result
-    in not using the data for fitting, but it will be plotted.
-    Another sensible argument would be "'ok','no fit','?'", in order to additionally
-    retrieve data which has not yet been checked.}
+    With the default value "'ok','no fit'", only data that has been checked and
+    set to "ok" or "no fit" in the database is retrieved. The argument "no fit"
+    will result in not using the data for fitting, but it will be plotted.
+    Another sensible argument would be "'ok','no fit','?'", in order to
+    additionally retrieve data which has not yet been checked.}
 }
 \value{
   \item{data}{
-    A data frame with a factor describing the dose levels, the numeric dose levels
-    and a numeric column describing the response, as well as the entries for
-    plate, experimentator, performed (date of test performance), celltype, unit
-    (of the dose/concentration), and for the ok field in the database.}
+    A data frame with a factor describing the dose levels, the numeric dose
+    levels and a numeric column describing the response, as well as the entries
+    for plate, experimentator, performed (date of test performance), celltype,
+    unit (of the dose/concentration), and for the ok field in the database.}
 }
 \details{
   The function is currently only used for retrieving data from the
@@ -74,11 +75,12 @@
     Database \tab = \tab cytotox  \cr
     Server \tab = \tab eckehaat  \cr
     Port \tab = \tab 3306  \cr
-  }.
+  }
 }
 \examples{
-# Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81 cells
-\dontrun{data <- drdata(c("TBT","ZnPT2"))}
+# Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81
+# cells
+\dontrun{drdata(c("TBT","ZnPT2"))}
 }
 \author{
   Johannes Ranke 
diff --git a/man/drfit-package.Rd b/man/drfit-package.Rd
index d98e10e..43334ff 100644
--- a/man/drfit-package.Rd
+++ b/man/drfit-package.Rd
@@ -13,14 +13,16 @@ There is a preliminary version of an introductory article located in \url{../doc
 \author{
 Author and Maintainer: Johannes Ranke <jranke@uni-bremen.de>
 }
+\note{There is a demo for each dataset that can be accessed by
+  \code{demo(dataset)}} 
 \keyword{ package }
 \keyword{ models }
 \keyword{ regression }
 \keyword{ nonlinear }
 \seealso{
-There is another, more statistically sophisticated package with similar
-functionality called \code{\link[drc:drc-package]{drc}}. I think my package is
-more user-friendly, though.
+On CRAN, there is another, more statistically sophisticated package with
+similar functionality called \code{\link[drc:drc-package]{drc}}. I think 
+the advantage of my package is its user-friendliness.
 }
 \examples{
 data(antifoul)
diff --git a/man/drfit.Rd b/man/drfit.Rd
index 9eb5476..a89b5dd 100644
--- a/man/drfit.Rd
+++ b/man/drfit.Rd
@@ -100,6 +100,8 @@ data(antifoul)
 r <- drfit(antifoul)
 format(r,digits=2)
 }
+\note{There is a demo for each dataset that can be accessed by
+  \code{demo(dataset)}} 
 \author{
   Johannes Ranke 
   \email{jranke@uni-bremen.de} 
diff --git a/man/drplot.Rd b/man/drplot.Rd
index f8f8aa8..bff2388 100644
--- a/man/drplot.Rd
+++ b/man/drplot.Rd
@@ -49,9 +49,7 @@
     }
   \item{overlay}{
     If TRUE, all output will be put into one graph, otherwise a separate graph
-    will be created for each substance. In the latter case, on-screen display
-    (postscript=FALSE) only works correctly for data plots. Dose-response models
-    will all be put into the last graph in this case.
+    will be created for each substance. 
     }
   \item{xlim}{
     The plot limits (min,max) on the dose axis.
@@ -66,7 +64,7 @@
     }
   \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
+    the postscript, and png arguments are also FALSE, graphics will be
     displayed with a screen graphics device.
     }
   \item{png}{
@@ -79,7 +77,7 @@
     is TRUE.
     }
   \item{pointsize}{
-    The pointsize used for png and postscript graphics.
+    The pointsize used for pdf, png and postscript graphics.
     }
   \item{colors}{
     This is a vector of colors, defaulting to 1:8, used for plotting the data.
@@ -89,26 +87,24 @@
     of the legend by being passed to the legend function. See the help for the
     legend function for all possiblities.} 
   \item{devoff}{
-    If set to FALSE, the closing of the device after creation of an overlay png
-    or postscript graph will be left out, so texts and other elements can be 
-    added to the graph.
+    If set to FALSE, the device will not be closed after creation of an overlay
+    pdf, png or postscript graph, so texts and other elements can
+    be added.
     }
 }
 \value{
   \item{results}{
     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.
+    screen and/or as postscript/pdf/png files, depending on the parameters.
     }
 } 
-\note{
-  Be sure all devices are closed (e.g. by calling \code{dev.off()}) before
-  calling \code{drplot} again after a failure.
-}
 \examples{
 data(antifoul)
 r <- drfit(antifoul)
 \dontrun{drplot(r,antifoul)}
 }
+\note{There is a demo for each dataset that can be accessed by
+  \code{demo(dataset)}} 
 \author{
   Johannes Ranke 
   \email{jranke@uni-bremen.de} 
diff --git a/man/pyrithione.Rd b/man/pyrithione.Rd
index b24a906..f2d3064 100644
--- a/man/pyrithione.Rd
+++ b/man/pyrithione.Rd
@@ -11,6 +11,9 @@
 \format{
   A dataframe containing the data as required for the \code{\link{drfit}}
   function.  }
+\examples{
+  \dontrun{demo(pyrithione)}
+}
 \source{
   Doose C, Ranke J, Stock F, Bottin-Weber U, Jastorff B (2004)
   Structure-activity relationships of pyrithiones - IPC-81 toxicity tests with