Added the pyrithione and IM1x V. fischeri data with documentation

and cleaned the antioul data from some unnecessary components.



git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@58 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc

11 files changed, 68 insertions, 22 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 11639f2..c744e02 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,23 +1,20 @@
 Package: drfit
-Version: 0.04-57
-Date: 2006-03-04
+Version: 0.04-58
+Date: 2006-03-16
 Title: Dose-response data evaluation
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Maintainer: Johannes Ranke <jranke@uni-bremen.de>
 Depends: R (>= 2.1.0),stats,RODBC
-Description: drfit provides basic functions for fitting dose-response curves to
-	dose-response data, calculating some (eco)toxicological parameters and
-	plotting the results. Functions that are fitted are the cumulative densitiy
-	function of the lognormal distribution (probit fit), of the logistic
-	distribution (logit fit), of the weibull distribution (weibull fit) and
-	a linear-logistic model ("linlogit" fit), derived from the latter,
-	which is used to describe data showing stimulation at low doses
-	(hormesis). 
+Description: drfit provides basic and easy-to-use functions for fitting
+	dose-response curves to dose-response data, calculating some
+	(eco)toxicological parameters and plotting the results. Functions that are
+	fitted are the cumulative densitiy function of the lognormal distribution
+	(probit fit), of the logistic distribution (logit fit), of the weibull
+	distribution (weibull fit) and a linear-logistic model ("linlogit" fit),
+	derived from the latter, which is used to describe data showing stimulation
+	at low doses (hormesis). 
 	In addition, functions checking, plotting and retrieving dose-response data
 	retrieved from a database accessed via RODBC are included.
-	I would be delighted if you would join in this effort of creating useful
-	and useable tools for dealing with dose-response data from biological
-	testing.
 License: GPL version 2 or newer
 URL: http://www.r-project.org, 
 	http://www.uft.uni-bremen.de/chemie/ranke,
diff --git a/INDEX b/INDEX
index 3e1cc20..c02adfe 100644
--- a/INDEX
+++ b/INDEX
@@ -1,9 +1,13 @@
 antifoul                Dose-Response data for TBT and Zink Pyrithione
                         in IPC-81 cells
-checkplate              Check raw data from a specified microtiter
-                        plate
-checksubstance          Check raw data for a specified substance
 drdata                  Get dose-response data
 drfit                   Fit dose-response models
+drfit-package           Dose-response data evaluation
 drplot                  Plot dose-response models
-linearlogisf            Linear-logistic function
+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/drfit.R b/R/drfit.R
index 3a9535a..4d93a6d 100644
--- a/R/drfit.R
+++ b/R/drfit.R
@@ -300,7 +300,7 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
 drplot <- function(drresults, data, 
         dtype = "std", alpha = 0.95, ctype = "none",
         path = "./", fileprefix = "drplot", overlay = FALSE,
-        postscript = FALSE, png = FALSE, pdf = FALSE, 
+        postscript = FALSE, pdf = FALSE, png = FALSE, 
         bw = TRUE,
         pointsize = 12,
         colors = 1:8, devoff=T, lpos="topright")
diff --git a/data/IM1xVibrio.rda b/data/IM1xVibrio.rda
new file mode 100644
index 0000000..d49d2c6
--- /dev/null
+++ b/data/IM1xVibrio.rda
diff --git a/data/antifoul.rda b/data/antifoul.rda
index 5360fee..4fc0ba6 100644
--- a/data/antifoul.rda
+++ b/data/antifoul.rda
diff --git a/data/pyrithione.rda b/data/pyrithione.rda
new file mode 100644
index 0000000..0256679
--- /dev/null
+++ b/data/pyrithione.rda
diff --git a/man/IM1xVibrio.Rd b/man/IM1xVibrio.Rd
new file mode 100644
index 0000000..468fb67
--- /dev/null
+++ b/man/IM1xVibrio.Rd
@@ -0,0 +1,26 @@
+\name{IM1xVibrio}
+\docType{data}
+\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.
+}
+\usage{data(IM1xVibrio)}
+\format{
+  A dataframe containing the data as required for the \code{\link{drfit}} function. Additional
+  columns contain the name of the persons that generated the data
+  (\code{experimentator}) 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,
+  Ondruschka B, Filser J, Jastorff B (2004) Biological effects of imidazolium
+  ionic liquids with varying chain lenghts in acute Vibrio fischeri and WST-1
+  cell viability assays. Ecotoxicology and Environmental Safety 58(3) 396-404
+}
+\keyword{datasets}
diff --git a/man/antifoul.Rd b/man/antifoul.Rd
index daf7414..bebec41 100644
--- a/man/antifoul.Rd
+++ b/man/antifoul.Rd
@@ -11,8 +11,8 @@
 \usage{data(antifoul)}
 \format{
   A dataframe containing 135 and 81 data points for concentrations and responses
-  for TBT and Zink Pyrithione, respectively. Additional data from the database is 
-  also present.
+  for TBT and Zink Pyrithione, respectively. Some additional columns from the
+  database are also present.
 }
 \source{
   \url{http://www.uft.uni-bremen.de/chemie}
diff --git a/man/drfit-package.Rd b/man/drfit-package.Rd
index ac91a35..782849e 100644
--- a/man/drfit-package.Rd
+++ b/man/drfit-package.Rd
@@ -19,7 +19,7 @@ Author and Maintainer: Johannes Ranke <jranke@uni-bremen.de>
 \keyword{ nonlinear }
 \seealso{
 There is another, more sophisticated package with similar functionality
-called \code{\link[drc:drc-package]{drc}
+called \code{\link[drc:drc-package]{drc}}
 }
 \examples{
 data(antifoul)
diff --git a/man/drplot.Rd b/man/drplot.Rd
index 09a8517..4c9e298 100644
--- a/man/drplot.Rd
+++ b/man/drplot.Rd
@@ -7,7 +7,7 @@
 }
 \usage{
   drplot(drresults, data, dtype, alpha, ctype, path, fileprefix, overlay,
-    postscript, png, bw, pointsize, colors, devoff, lpos)
+    postscript, pdf, png, bw, pointsize, colors, devoff, lpos)
 }
 \arguments{
   \item{drresults}{
diff --git a/man/pyrithione.Rd b/man/pyrithione.Rd
new file mode 100644
index 0000000..4ea72cc
--- /dev/null
+++ b/man/pyrithione.Rd
@@ -0,0 +1,19 @@
+\name{pyrithione}
+\docType{data}
+\alias{pyrithione}
+\title{Cytotoxicity data for different pyrithionates and related species}
+\description{
+ This data shows the cytotoxicity of pyrithione salts as well as the free
+ pyrithione, its oxidation product and some other related compounds to the
+ IPC-81 cell line.
+}
+\usage{data(pyrithione)}
+\format{
+  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
+  antifouling biocide zinc pyrithione and structural analogues. Green Chemistry
+  6(5) 259-266 }
+\keyword{datasets}