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-rw-r--r--man/IM1xIPC81.Rd3
-rw-r--r--man/IM1xVibrio.Rd3
-rw-r--r--man/XY.Rd3
-rw-r--r--man/antifoul.Rd3
-rw-r--r--man/checkexperiment.Rd4
-rw-r--r--man/checksubstance.Rd12
-rw-r--r--man/drdata.Rd46
-rw-r--r--man/drfit-package.Rd8
-rw-r--r--man/drfit.Rd2
-rw-r--r--man/drplot.Rd22
-rw-r--r--man/pyrithione.Rd3
11 files changed, 64 insertions, 45 deletions
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 <jranke@uni-bremen.de>
}
+\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

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