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-rw-r--r--DESCRIPTION23
-rw-r--r--INDEX12
-rw-r--r--R/drfit.R2
-rw-r--r--data/IM1xVibrio.rdabin0 -> 10469 bytes
-rw-r--r--data/antifoul.rdabin12244 -> 10643 bytes
-rw-r--r--data/pyrithione.rdabin0 -> 54479 bytes
-rw-r--r--man/IM1xVibrio.Rd26
-rw-r--r--man/antifoul.Rd4
-rw-r--r--man/drfit-package.Rd2
-rw-r--r--man/drplot.Rd2
-rw-r--r--man/pyrithione.Rd19
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
Binary files differ
diff --git a/data/antifoul.rda b/data/antifoul.rda
index 5360fee..4fc0ba6 100644
--- a/data/antifoul.rda
+++ b/data/antifoul.rda
Binary files differ
diff --git a/data/pyrithione.rda b/data/pyrithione.rda
new file mode 100644
index 0000000..0256679
--- /dev/null
+++ b/data/pyrithione.rda
Binary files differ
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}

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