From 18b13d3122eaa4f803795dfa2cb5ba951c8354f6 Mon Sep 17 00:00:00 2001
From: "(no author)" <(no author)@d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc>
Date: Wed, 1 Sep 2004 05:05:20 +0000
Subject: Fixed some mistakes in the help files, and took away the dependency
 on the defunct nls package in the function drfit.

git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@4 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
---
 DESCRIPTION     |  4 ++--
 R/drfit.R       | 13 ++++++-------
 man/antifoul.Rd |  4 ++--
 man/drdata.Rd   |  9 +++++----
 man/drfit.Rd    |  6 +++---
 man/drplot.Rd   | 18 +++++++++++-------
 6 files changed, 29 insertions(+), 25 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 725fa50..7ba2f92 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: drfit
-Version: 0.02-3
-Date: 2004-07-23
+Version: 0.02-4
+Date: 2004-08-31
 Title: Dose-response data evaluation
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Maintainer: Johannes Ranke <jranke@uni-bremen.de>
diff --git a/R/drfit.R b/R/drfit.R
index c3fc945..a3b8a1b 100644
--- a/R/drfit.R
+++ b/R/drfit.R
@@ -23,13 +23,12 @@ drdata <- function(substances, experimentator = "%", db = "cytotox",
 drfit <- function(data, startlogEC50 = NA, lognorm = TRUE, logis = FALSE,
         linearlogis = FALSE, b0 = 2, f0 = 0)
 {
-    library(nls)
-        substances <- levels(data$substance)
-        unit <- levels(as.factor(data$unit))
-        logisf <- function(x,x0,b,k=1)
-        {
-            k / (1 + (x/x0)^b)
-        }
+    substances <- levels(data$substance)
+    unit <- levels(as.factor(data$unit))
+    logisf <- function(x,x0,b,k=1)
+    {
+        k / (1 + (x/x0)^b)
+    }
     linearlogisf <- function(x,k,f,mu,b)
     {
         k*(1 + f*x) / (1 + ((2*f*(10^mu) + 1) * ((x/(10^mu))^b)))
diff --git a/man/antifoul.Rd b/man/antifoul.Rd
index 2f4ae85..daf7414 100644
--- a/man/antifoul.Rd
+++ b/man/antifoul.Rd
@@ -8,10 +8,10 @@
   from the "cytotox" database of the UFT Department of Bioorganic Chemistry on 
   February 25, 2004
 }
-\usage{data(rivers)}
+\usage{data(antifoul)}
 \format{
   A dataframe containing 135 and 81 data points for concentrations and responses
-  for TBT and Zink Pyrithione, respecitively. Additional data from the database is 
+  for TBT and Zink Pyrithione, respectively. Additional data from the database is 
   also present.
 }
 \source{
diff --git a/man/drdata.Rd b/man/drdata.Rd
index b9f8660..dd62ff9 100644
--- a/man/drdata.Rd
+++ b/man/drdata.Rd
@@ -37,10 +37,11 @@
 \details{
   The function is currently only used for retrieving data from the
   mysql database "cytotox" of the UFT Department of Bioorganic Chemistry.
-  Additionally to the installation of the RODBC package, it is required to set
-  up a ODBC data source with the name "cytotox", using an ODBC driver for mysql, 
-  probably myODBC. Then, under Unix, you can use iodbc or unixodbc for setting
-  up the respective data source with data source name (DSN) "cytotox". For my
+  Access to this database is limited to UFT staff.  Additionally to the
+  installation of the RODBC package, it is required to set up a ODBC data
+  source with the name "cytotox", using an ODBC driver for mysql, probably
+  myODBC. Then, under Unix, you can use iodbc or unixodbc for setting up the
+  respective data source with data source name (DSN) "cytotox". For my
   setting using unixodbc, I am using the file \file{/etc/odbcinst.ini}
   containing: 
   \tabular{lll}{
diff --git a/man/drfit.Rd b/man/drfit.Rd
index 6e39032..f9843f5 100644
--- a/man/drfit.Rd
+++ b/man/drfit.Rd
@@ -45,9 +45,9 @@
     
 } 
 \examples{
-\dontrun{data(antifoul)}
-\dontrun{r <- drfit(antifoul)}
-\dontrun{format(r,digits=2)}
+data(antifoul)
+r <- drfit(antifoul)
+format(r,digits=2)
 }
 \author{
   Johannes Ranke 
diff --git a/man/drplot.Rd b/man/drplot.Rd
index bb4826e..f201332 100644
--- a/man/drplot.Rd
+++ b/man/drplot.Rd
@@ -65,16 +65,20 @@
 }
 \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 "none".
-      Every successful fit is reported in one line. Parameters of the fitted curves are only
-      reported if the fitted EC50 is not higher than the highest dose.}
+    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{
+  Turn off the colors if you don't like them and don't want to fiddle with
+  them. Treatment of legends is quite bad. Be sure all devices are closed
+  (e.g. by calling \code{dev.off()}) before calling \code{drplot} again.
+}
 \examples{
-\dontrun{data(antifoul)}
-\dontrun{r <- drfit(antifoul)}
-\dontrun{format(r,digits=2)}
+data(antifoul)
+r <- drfit(antifoul)
+\dontrun{drplot(r,antifoul)}
 }
 \author{
   Johannes Ranke 
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