First version published on CRAN

git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@1 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc

4 files changed, 239 insertions, 0 deletions

diff --git a/man/antifoul.Rd b/man/antifoul.Rd
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+\name{antifoul}
+\docType{data}
+\alias{antifoul}
+\title{Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells}
+\description{
+  This data set shows the response of the rat leukaemic cell line IPC-81 to 
+  dilution series of tributyltin chloride (TBT) and Zink Pyrithione as retrieved
+  from the "cytotox" database of the UFT Department of Bioorganic Chemistry on 
+  February 25, 2004
+}
+\usage{data(rivers)}
+\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 
+  also present.
+}
+\source{
+  \url{http://www.uft.uni-bremen.de/chemie}
+}
+\keyword{datasets}
diff --git a/man/drdata.Rd b/man/drdata.Rd
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+++ b/man/drdata.Rd
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+\name{drdata}
+\alias{drdata}
+\title{Get dose-response data}
+\description{
+	Get dose-response data from a remote mysql server 
+}
+\usage{
+  drdata(substances, experimentator = "\%", db = "cytotox", celltype = "IPC-81", 
+    whereClause = "1", ok = "'ok'")
+}
+\arguments{
+  \item{substances}{
+    A string or an array of strings with the substance names for
+    which dose-response data is to be retrieved.}
+  \item{experimentator}{
+    The name of the experimentator whose data is to be used.}
+  \item{db}{
+    The database to be used. Currently only "cytotox" of the UFT Department of
+    Bioorganic Chemistry is supported.}
+  \item{celltype}{
+    Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are supported.}
+  \item{whereClause}{
+    With this argument, additional conditions for the SQL query can be set, 
+    e.g. "where plate != 710". The default is 1 (in SQL syntax this means TRUE).}
+  \item{ok}{
+    With the default value "'ok'", only data that has been checked and set to "ok"
+    in the database is retrieved. Another sensible argument would be "'ok','?'", in 
+    order to additionally retrieve data which has not yet been checked.}
+}
+\value{
+  \item{data}{
+    A data frame with a factor describing the dose levels, the numeric dose levels
+    and a numeric column describing the response, as well as the entries for
+    plate, experimentator, performed (date of test performance), celltype, unit
+    (of the dose/concentration), and for the ok field in the database.}
+}
+\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
+  setting using unixodbc, I am using the file \file{/etc/odbcinst.ini}
+  containing: 
+  \tabular{lll}{
+    [MySQL] \tab \tab \cr
+    Description \tab = \tab MySQL driver for ODBC \cr
+    Driver \tab = \tab /usr/local/lib/libmyodbc.so \cr
+    Setup \tab = \tab /usr/lib/odbc/libodbcmyS.so \cr
+  }
+  and the file \file{/etc/odbc.ini} containing:
+  \tabular{lll}{
+    [cytotox] \tab \tab \cr
+    Description \tab = \tab Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen \cr
+    Driver \tab = \tab MySQL \cr
+    Trace \tab = \tab Yes  \cr
+    TraceFile \tab = \tab /tmp/odbc.log  \cr
+    Database \tab = \tab cytotox  \cr
+    Server \tab = \tab eckehaat  \cr
+    Port \tab = \tab 3306  \cr
+  }.
+}
+\examples{
+# Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81 cells
+\dontrun{data <- drdata(c("TBT","Zn Pyrithion"))}
+}
+\author{
+  Johannes Ranke 
+  \email{jranke@uni-bremen.de} 
+  \url{http://www.uft.uni-bremen.de/chemie/ranke}
+}
+\keyword{IO}
+\keyword{database}
diff --git a/man/drfit.Rd b/man/drfit.Rd
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+++ b/man/drfit.Rd
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+\name{drfit}
+\alias{drfit}
+\title{Fit dose-response models}
+\description{
+	Fit dose-response relationships to dose-response data and calculate
+  biometric results for (eco)toxicity evaluation
+}
+\usage{
+  drfit(data, startlogEC50 = NA, lognorm = TRUE, logis = FALSE, 
+    linearlogis = FALSE, b0 = 2, f0 = 0)
+}
+\arguments{
+  \item{data}{
+    A data frame as returned from \code{\link{drdata}}.  The data frame has to
+    contain at least a factor called "substance", a vector called "unit"
+    containing the unit used for the dose, a column "response" with the
+    response values of the test system normalized between 0 and 1 and a column
+    "dose" with the numeric dose values. For later use of the
+    \code{\link{drplot}} function, a factor called "dosefactor" also has to be
+    present, containing the dose as a factor.
+    }
+  \item{startlogEC50}{
+    Especially for the linearlogis model, a suitable log10 of the EC50 has to be given 
+    by the user, since it is not correctly estimated for data showing hormesis with
+    the default estimation method.}
+  \item{lognorm}{
+    A boolean defining if cumulative density curves of normal distributions
+    are fitted to the data. Default ist TRUE.} 
+  \item{logis}{
+    A boolean defining if cumulative densitiy curves of logistic distributions
+    are fitted to the data. Default is FALSE.} 
+  \item{linearlogis}{
+    A boolean defining if the linear-logistic function as defined by van Ewijk and Hoekstra
+    1993 is fitted to the data. Default is FALSE.}
+  \item{b0,f0}{
+    If the linearlogistic model is fitted, b0 and f0 give the possibility to
+    adapt the starting values for the parameters b and f.}
+}
+\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.}
+    
+} 
+\examples{
+\dontrun{data(antifoul)}
+\dontrun{r <- drfit(antifoul)}
+\dontrun{format(r,digits=2)}
+}
+\author{
+  Johannes Ranke 
+  \email{jranke@uni-bremen.de} 
+  \url{http://www.uft.uni-bremen.de/chemie/ranke}
+}
+\keyword{models}
+\keyword{regression}
+\keyword{nonlinear}
diff --git a/man/drplot.Rd b/man/drplot.Rd
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+++ b/man/drplot.Rd
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+\name{drplot}
+\alias{drplot}
+\title{Plot dose-response models}
+\description{
+	Produce graphics of dose-response data and dose-response relationships 
+  either combined or separately, for one or more substances.
+}
+\usage{
+  drplot(drresults, data, dtype, alpha, path, fileprefix, overlay,
+    postscript, color, colors, fitcolors)
+}
+\arguments{
+  \item{drresults}{
+    A data frame as returned from \code{\link{drfit}}.
+    }
+  \item{data}{ 
+    A data frame as returned from \code{\link{drdata}}.  If data is to be
+    plotted, the data frame has to contain at least a factor called
+    "substance", a vector called "unit" containing the unit used for the dose,
+    a column "response" with the response values of the test system normalized
+    between 0 and 1, a column "dose" with the numeric dose values and a factor
+    called "dosefactor" containing the dose as a factor. If plotting of the data is 
+    not required, data can be set to FALSE.
+    }
+  \item{dtype}{
+    A string describing if the raw data should be plotted ("raw"), or 
+    an error bar should be constructed from the standard deviations of the
+    responses at each dose level ("std", default value) or from the confidence
+    intervals ("conf"). Of course, dtype only makes a difference, if a valid data
+    object has been referenced.
+    }
+  \item{alpha}{
+    The confidence level, defaulting to 0.95, only used if dtype "conf" has been
+    chosen.
+    }
+  \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".
+    }
+  \item{overlay}{
+    If TRUE, all output will be put into one graph, otherwise a separate graph
+    will be created for each substance. In the latter case, on-screen display
+    (postscript=FALSE) only works correctly for data plots. Dose-response models
+    will all be put into the last graph in this case.
+    }
+  \item{postscript}{
+    If TRUE, (a) postscript graph(s) will be created. Otherwise, graphics will be
+    displayed with a screen graphics device.
+    }
+  \item{color}{
+    If TRUE, a sensible selection of colors will be attempted. If false, everything
+    will be drawn in black
+    }
+  \item{colors}{
+    This is a vector of colors, defaulting to 1:8, used for plotting the data.
+    }
+  \item{fitcolors}{
+    Here you can specify a palette for the colors of the dose-response fits. The 
+    default value is "default", which produces rainbow colors.
+    }
+}
+\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.}
+    
+} 
+\examples{
+\dontrun{data(antifoul)}
+\dontrun{r <- drfit(antifoul)}
+\dontrun{format(r,digits=2)}
+}
+\author{
+  Johannes Ranke 
+  \email{jranke@uni-bremen.de} 
+  \url{http://www.uft.uni-bremen.de/chemie/ranke}
+}
+\keyword{models}
+\keyword{regression}
+\keyword{nonlinear}