diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/antifoul.Rd | 20 | ||||
| -rw-r--r-- | man/drdata.Rd | 74 | ||||
| -rw-r--r-- | man/drfit.Rd | 59 | ||||
| -rw-r--r-- | man/drplot.Rd | 86 |
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} |