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| -rw-r--r-- | DESCRIPTION | 23 | ||||
| -rw-r--r-- | INDEX | 12 | ||||
| -rw-r--r-- | R/drfit.R | 2 | ||||
| -rw-r--r-- | data/IM1xVibrio.rda | bin | 0 -> 10469 bytes | |||
| -rw-r--r-- | data/antifoul.rda | bin | 12244 -> 10643 bytes | |||
| -rw-r--r-- | data/pyrithione.rda | bin | 0 -> 54479 bytes | |||
| -rw-r--r-- | man/IM1xVibrio.Rd | 26 | ||||
| -rw-r--r-- | man/antifoul.Rd | 4 | ||||
| -rw-r--r-- | man/drfit-package.Rd | 2 | ||||
| -rw-r--r-- | man/drplot.Rd | 2 | ||||
| -rw-r--r-- | man/pyrithione.Rd | 19 |
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, @@ -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 @@ -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 Binary files differnew file mode 100644 index 0000000..d49d2c6 --- /dev/null +++ b/data/IM1xVibrio.rda diff --git a/data/antifoul.rda b/data/antifoul.rda Binary files differindex 5360fee..4fc0ba6 100644 --- a/data/antifoul.rda +++ b/data/antifoul.rda diff --git a/data/pyrithione.rda b/data/pyrithione.rda Binary files differnew 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} |