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-rw-r--r--man/antifoul.Rd20
-rw-r--r--man/drdata.Rd74
-rw-r--r--man/drfit.Rd59
-rw-r--r--man/drplot.Rd86
4 files changed, 239 insertions, 0 deletions
diff --git a/man/antifoul.Rd b/man/antifoul.Rd
new file mode 100644
index 0000000..2f4ae85
--- /dev/null
+++ b/man/antifoul.Rd
@@ -0,0 +1,20 @@
+\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
new file mode 100644
index 0000000..b9f8660
--- /dev/null
+++ b/man/drdata.Rd
@@ -0,0 +1,74 @@
+\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
new file mode 100644
index 0000000..6e39032
--- /dev/null
+++ b/man/drfit.Rd
@@ -0,0 +1,59 @@
+\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
new file mode 100644
index 0000000..bb4826e
--- /dev/null
+++ b/man/drplot.Rd
@@ -0,0 +1,86 @@
+\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}

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