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.
+
+
+
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+Get dose-response data
+
+
+
+
+
drdata(drfit)
R Documentation
+
+
+
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
+
+
+
substances
+
+A string or an array of strings with the substance names for
+which dose-response data is to be retrieved.
+
experimentator
+
+The name of the experimentator whose data is to be used.
+
db
+
+The database to be used. Currently only "cytotox" of the UFT Department of
+Bioorganic Chemistry is supported.
+
celltype
+
+Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are supported.
+
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).
+
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.
+
+
+
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 ‘/etc/odbcinst.ini’
+containing:
+
+
+
[MySQL]
+
+
+
Description
=
MySQL driver for ODBC
+
+
+
Driver
=
/usr/local/lib/libmyodbc.so
+
+
+
Setup
=
/usr/lib/odbc/libodbcmyS.so
+
+
+
+and the file ‘/etc/odbc.ini’ containing:
+
+
+
[cytotox]
+
+
+
Description
=
Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen
+
+
+
Driver
=
MySQL
+
+
+
Trace
=
Yes
+
+
+
TraceFile
=
/tmp/odbc.log
+
+
+
Database
=
cytotox
+
+
+
Server
=
eckehaat
+
+
+
Port
=
3306
+
+
+.
+
+
+
+
Value
+
+
+
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 as returned from 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
+drplot function, a factor called "dosefactor" also has to be
+present, containing the dose as a factor.
+
+
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.
+
lognorm
+
+A boolean defining if cumulative density curves of normal distributions
+are fitted to the data. Default ist TRUE.
+
logis
+
+A boolean defining if cumulative densitiy curves of logistic distributions
+are fitted to the data. Default is FALSE.
+
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.
+
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
+
+
+
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.
+A data frame as returned from 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.
+
+
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.
+
+
alpha
+
+The confidence level, defaulting to 0.95, only used if dtype "conf" has been
+chosen.
+
+
path
+
+The path where graphic files should be put if any are produced. Defaults
+to "./" i.e. the current working directory of R.
+
+
fileprefix
+
+A string which will form the beginning of each filename, if graphic files are
+created. Defaults to "drplot".
+
+
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.
+
+
postscript
+
+If TRUE, (a) postscript graph(s) will be created. Otherwise, graphics will be
+displayed with a screen graphics device.
+
+
color
+
+If TRUE, a sensible selection of colors will be attempted. If false, everything
+will be drawn in black
+
+
colors
+
+This is a vector of colors, defaulting to 1:8, used for plotting the data.
+
+
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
+
+
+
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.
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