- drplot: Removed the call to get(getOption("device")), since it caused

  problems when calling drplot from Sweave code chunks as well as in JGR.
- drplot: Removed the output with cat, since it may be annoying to receive
  a message when a plot was requested
- Small documentation adaptations and fixes



git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@70 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc

5 files changed, 28 insertions, 33 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index db0927f..84afd13 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: drfit
-Version: 0.05-68
-Date: 2006-04-21
+Version: 0.05-70
+Date: 2006-04-26
 Title: Dose-response data evaluation
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Maintainer: Johannes Ranke <jranke@uni-bremen.de>
diff --git a/INDEX b/INDEX
index b59f306..46556eb 100644
--- a/INDEX
+++ b/INDEX
@@ -1,10 +1,3 @@
-IM1xIPC81               Dose-Response data for
-                        1-methyl-3-alkylimidazolium tetrafluoroborates
-                        in IPC-81 cells
-IM1xVibrio              Dose-Response data for
-                        1-methyl-3-alkylimidazolium tetrafluoroborates
-                        in V. fischeri
-XY                      Dose-Response data for two substances X and Y
 antifoul                Dose-Response data for TBT and Zink Pyrithione
                         in IPC-81 cells
 checkexperiment         Check raw data from a specified experiment or
@@ -13,6 +6,13 @@ drdata                  Get dose-response data
 drfit                   Fit dose-response models
 drfit-package           Dose-response data evaluation
 drplot                  Plot dose-response models
+IM1xIPC81               Dose-Response data for
+                        1-methyl-3-alkylimidazolium tetrafluoroborates
+                        in IPC-81 cells
+IM1xVibrio              Dose-Response data for
+                        1-methyl-3-alkylimidazolium tetrafluoroborates
+                        in V. fischeri
 linlogitf               Linear-logistic function
 pyrithione              Cytotoxicity data for different pyrithionates
                         and related species
+XY                      Dose-Response data for two substances X and Y
diff --git a/R/drplot.R b/R/drplot.R
index 8faaa0f..eaae85b 100644
--- a/R/drplot.R
+++ b/R/drplot.R
@@ -25,12 +25,7 @@ drplot <- function(drresults, data,
         if (nc > 0) {
             sdc <- sd(zerodata$response)
             controlconf <- sdc * qt((1 + alpha)/2, nc - 1) / sqrt(nc)
-            cat("There are ",nc,"data points with dose 0 (control values)\n")
-            cat("with a standard deviation of",sdc,"\n")
-            cat("and a confidence interval of",controlconf,"\n")
             if (nc < 3) {
-                cat("\nThere are less than 3 control points, therefore their scatter\n")
-                cat("will not be displayed\n")
                 ctype = "none"
             }
         } else {
@@ -82,15 +77,17 @@ drplot <- function(drresults, data,
                 width=500, height=500, pointsize=pointsize)
             cat("Created File: ",filename,"\n")
         }
-        if (!postscript && !png && !pdf) {
-            get(getOption("device"))(width=7,height=7)
-        }
             
         plot(0,type="n",
             xlim = xlim,
             ylim = ylim,
             xlab = paste("Decadic Logarithm of the dose in ", unit),    
             ylab = "Normalized response")
+    } else {
+        # If overlay plot is not requested, ask before showing multiple plots on the screen
+        if (!postscript && !png && !pdf) {
+            par(ask=TRUE)
+        }
     }
 
     # Plot the data either as raw data or as error bars
@@ -126,9 +123,6 @@ drplot <- function(drresults, data,
                             width=500, height=500, pointsize=pointsize)
                         cat("Created File: ",filename,"\n")
                     }
-                    if (!postscript && !png && !pdf) {
-                         get(getOption("device"))(width=7,height=7)
-                    }
                         
                     plot(0,type="n",
                         xlim = xlim,
diff --git a/man/drfit.Rd b/man/drfit.Rd
index afbf40b..fefea85 100644
--- a/man/drfit.Rd
+++ b/man/drfit.Rd
@@ -69,8 +69,8 @@
   \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
+	  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. 
@@ -84,14 +84,14 @@
 	  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
+	  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
+	  \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
+	  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.}
 } 
diff --git a/man/drplot.Rd b/man/drplot.Rd
index 0249476..2f1d4ae 100644
--- a/man/drplot.Rd
+++ b/man/drplot.Rd
@@ -34,17 +34,18 @@
     }
   \item{ctype}{
     This argument decides if horizontal lines are drawn to show the scatter of 
-    the control values (dose = 0, mean response = 1). 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