From 6d220f8d71564a0430473ab2465e169adddb02d8 Mon Sep 17 00:00:00 2001 From: ranke Date: Fri, 28 Apr 2006 11:42:14 +0000 Subject: - Fixed the drplot function, so the graphics parameter ask is adequately set depending on the overlay argument, and set back to the previous value - Added a test for each datase - Added a demo for each dataset - Corrected many small bugs in the documentation and improved formatting of the .Rd files git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@74 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc --- man/IM1xIPC81.Rd | 3 +++ man/IM1xVibrio.Rd | 3 +++ man/XY.Rd | 3 +++ man/antifoul.Rd | 3 +++ man/checkexperiment.Rd | 4 ++-- man/checksubstance.Rd | 12 +++++++----- man/drdata.Rd | 46 ++++++++++++++++++++++++---------------------- man/drfit-package.Rd | 8 +++++--- man/drfit.Rd | 2 ++ man/drplot.Rd | 22 +++++++++------------- man/pyrithione.Rd | 3 +++ 11 files changed, 64 insertions(+), 45 deletions(-) (limited to 'man') diff --git a/man/IM1xIPC81.Rd b/man/IM1xIPC81.Rd index 40aaa81..4f5a1dd 100644 --- a/man/IM1xIPC81.Rd +++ b/man/IM1xIPC81.Rd @@ -20,6 +20,9 @@ \code{\link{drfit}} function. An additional column contains the tested organism (name of the cell line). } +\examples{ + \dontrun{demo(IM1xIPC81)} +} \source{ Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J, Hoffmann J, Ondruschka B, Filser J, Jastorff B (2004) diff --git a/man/IM1xVibrio.Rd b/man/IM1xVibrio.Rd index 454e099..5315432 100644 --- a/man/IM1xVibrio.Rd +++ b/man/IM1xVibrio.Rd @@ -18,6 +18,9 @@ Vibrio fischeri, \code{organism}), and a field specifying if the data is regarded valid (\code{ok}). } +\examples{ + \dontrun{demo(IM1xVibrio)} +} \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 diff --git a/man/XY.Rd b/man/XY.Rd index ab304ba..8022264 100644 --- a/man/XY.Rd +++ b/man/XY.Rd @@ -11,6 +11,9 @@ A dataframe containing dose (concentration) and response data, as well as control values where the dose is zero. } +\examples{ + \dontrun{demo(XY)} +} \source{ \url{http://www.uft.uni-bremen.de/chemie} } diff --git a/man/antifoul.Rd b/man/antifoul.Rd index bebec41..2aa532e 100644 --- a/man/antifoul.Rd +++ b/man/antifoul.Rd @@ -14,6 +14,9 @@ for TBT and Zink Pyrithione, respectively. Some additional columns from the database are also present. } +\examples{ + \dontrun{demo(antifoul)} +} \source{ \url{http://www.uft.uni-bremen.de/chemie} } diff --git a/man/checkexperiment.Rd b/man/checkexperiment.Rd index d68cd87..56db90c 100644 --- a/man/checkexperiment.Rd +++ b/man/checkexperiment.Rd @@ -22,8 +22,8 @@ The function lists a report and shows two graphs side by side. } \examples{ -# Check plate number 1 in the cytotox database -\dontrun{data <- checkplate(3)} +# Check plate number 3 in the cytotox database +\dontrun{checkplate(3)} } \author{ Johannes Ranke diff --git a/man/checksubstance.Rd b/man/checksubstance.Rd index 59759e8..f5340fe 100644 --- a/man/checksubstance.Rd +++ b/man/checksubstance.Rd @@ -16,13 +16,15 @@ of the UFT Department of Bioorganic Chemistry are supported (default is "cytotox").} \item{experimentator}{ - The name of the experimentator whose data is to be used. Default is "\%", which - means that data from all experimentators are shown.} + The name of the experimentator whose data is to be used. Default is "\%", + which means that data from all experimentators are shown.} \item{celltype}{ - Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are supported. - Default is "\%", i.e. data for any cell type will be displayed.} + Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are + supported. Default is "\%", i.e. data for any cell type will be + displayed.} \item{enzymetype}{ - Currently, only data for AChE, GR and GST are supported. The default value is "\%", i.e. data for any enzyme type will be displayed.} + Currently, only data for AChE, GR and GST are supported. The default value + is "\%", i.e. data for any enzyme type will be displayed.} \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).} diff --git a/man/drdata.Rd b/man/drdata.Rd index 0c1e901..8f545da 100644 --- a/man/drdata.Rd +++ b/man/drdata.Rd @@ -1,8 +1,8 @@ \name{drdata} \alias{drdata} -\title{Get dose-response data} +\title{Get dose-response data via RODBC} \description{ - Get dose-response data from a remote mysql server + Get dose-response data from an adequate ODBC data source } \usage{ drdata(substances, experimentator = "\%", db = "cytotox", celltype = "IPC-81", @@ -14,39 +14,40 @@ 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. Default is "%", which - means that data from all experimentators are retrieved.} + The name of the experimentator whose data is to be used. Default is "%", + which means that data from all experimentators are retrieved.} \item{db}{ - The database to be used. Currently, the databases "cytotox" and "enzymes" - of the UFT Department of Bioorganic Chemistry are supported (default is - "cytotox").} + The database to be used. Currently, the databases "cytotox", "enzymes" + and "ecotox" of the UFT Department of Bioorganic Chemistry are + supported (default is "cytotox").} \item{celltype}{ - Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are supported.} + Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are + supported.} \item{enzymetype}{ Currently, only data for AChE, GR and GST are supported.} \item{organism}{ The organism that was exposed to the chemical. Only important if the database "ecotox" is used. Defaults to "Vibrio fischeri".} \item{endpoint}{ - The endpoint that should be used for selecting the data. Only important if the - database "ecotox" is used. Defaults to "Vibrio fischeri".} + The endpoint that should be used for selecting the data. Only important if + the database "ecotox" is used. Defaults to "Luminescence".} \item{whereClause}{ With this argument, additional conditions for the SQL query can be set, e.g. "plate != 710" (i.e. "Do not retrieve data for plate 710"). The default is 1 (in SQL syntax this means TRUE).} \item{ok}{ - With the default value "'ok','no fit'", only data that has been checked and set to "ok" - or "no fit" in the database is retrieved. The argument "no fit" will result - in not using the data for fitting, but it will be plotted. - Another sensible argument would be "'ok','no fit','?'", in order to additionally - retrieve data which has not yet been checked.} + With the default value "'ok','no fit'", only data that has been checked and + set to "ok" or "no fit" in the database is retrieved. The argument "no fit" + will result in not using the data for fitting, but it will be plotted. + Another sensible argument would be "'ok','no fit','?'", 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.} + 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 @@ -74,11 +75,12 @@ 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","ZnPT2"))} +# Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81 +# cells +\dontrun{drdata(c("TBT","ZnPT2"))} } \author{ Johannes Ranke diff --git a/man/drfit-package.Rd b/man/drfit-package.Rd index d98e10e..43334ff 100644 --- a/man/drfit-package.Rd +++ b/man/drfit-package.Rd @@ -13,14 +13,16 @@ There is a preliminary version of an introductory article located in \url{../doc \author{ Author and Maintainer: Johannes Ranke } +\note{There is a demo for each dataset that can be accessed by + \code{demo(dataset)}} \keyword{ package } \keyword{ models } \keyword{ regression } \keyword{ nonlinear } \seealso{ -There is another, more statistically sophisticated package with similar -functionality called \code{\link[drc:drc-package]{drc}}. I think my package is -more user-friendly, though. +On CRAN, there is another, more statistically sophisticated package with +similar functionality called \code{\link[drc:drc-package]{drc}}. I think +the advantage of my package is its user-friendliness. } \examples{ data(antifoul) diff --git a/man/drfit.Rd b/man/drfit.Rd index 9eb5476..a89b5dd 100644 --- a/man/drfit.Rd +++ b/man/drfit.Rd @@ -100,6 +100,8 @@ data(antifoul) r <- drfit(antifoul) format(r,digits=2) } +\note{There is a demo for each dataset that can be accessed by + \code{demo(dataset)}} \author{ Johannes Ranke \email{jranke@uni-bremen.de} diff --git a/man/drplot.Rd b/man/drplot.Rd index f8f8aa8..bff2388 100644 --- a/man/drplot.Rd +++ b/man/drplot.Rd @@ -49,9 +49,7 @@ } \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. + will be created for each substance. } \item{xlim}{ The plot limits (min,max) on the dose axis. @@ -66,7 +64,7 @@ } \item{pdf}{ If TRUE, (a) pdf graph(s) will be created. Otherwise, and if - the postscript and png arguments are also FALSE, graphics will be + the postscript, and png arguments are also FALSE, graphics will be displayed with a screen graphics device. } \item{png}{ @@ -79,7 +77,7 @@ is TRUE. } \item{pointsize}{ - The pointsize used for png and postscript graphics. + The pointsize used for pdf, png and postscript graphics. } \item{colors}{ This is a vector of colors, defaulting to 1:8, used for plotting the data. @@ -89,26 +87,24 @@ of the legend by being passed to the legend function. See the help for the legend function for all possiblities.} \item{devoff}{ - If set to FALSE, the closing of the device after creation of an overlay png - or postscript graph will be left out, so texts and other elements can be - added to the graph. + If set to FALSE, the device will not be closed after creation of an overlay + pdf, png or postscript graph, so texts and other elements can + be added. } } \value{ \item{results}{ You will get plots of data and/or the fitted dose-response curves, on the - screen and/or as postscript files, depending on the parameters. + screen and/or as postscript/pdf/png files, depending on the parameters. } } -\note{ - Be sure all devices are closed (e.g. by calling \code{dev.off()}) before - calling \code{drplot} again after a failure. -} \examples{ data(antifoul) r <- drfit(antifoul) \dontrun{drplot(r,antifoul)} } +\note{There is a demo for each dataset that can be accessed by + \code{demo(dataset)}} \author{ Johannes Ranke \email{jranke@uni-bremen.de} diff --git a/man/pyrithione.Rd b/man/pyrithione.Rd index b24a906..f2d3064 100644 --- a/man/pyrithione.Rd +++ b/man/pyrithione.Rd @@ -11,6 +11,9 @@ \format{ A dataframe containing the data as required for the \code{\link{drfit}} function. } +\examples{ + \dontrun{demo(pyrithione)} +} \source{ Doose C, Ranke J, Stock F, Bottin-Weber U, Jastorff B (2004) Structure-activity relationships of pyrithiones - IPC-81 toxicity tests with -- cgit v1.2.1