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-rw-r--r--chm/00Index.html24
-rw-r--r--chm/Rchm.css25
-rw-r--r--chm/antifoul.html49
-rw-r--r--chm/drdata.html146
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-rw-r--r--chm/drfit.hhp17
-rw-r--r--chm/drfit.html99
-rw-r--r--chm/drfit.toc51
-rw-r--r--chm/drplot.html131
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diff --git a/chm/00Index.html b/chm/00Index.html
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+<html><head><title>Dose-response data evaluation</title>
+<link rel="stylesheet" type="text/css" href="Rchm.css">
+</head><body>
+<h1>Dose-response data evaluation
+<img class="toplogo" src="logo.jpg" alt="[R logo]"></h1>
+
+<hr>
+
+<object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">
+<param name="keyword" value=".. contents">
+</object>
+
+
+<table width="100%">
+<tr><td width="25%"><a href="antifoul.html">antifoul</a></td>
+<td>Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells</td></tr>
+<tr><td width="25%"><a href="drdata.html">drdata</a></td>
+<td>Get dose-response data</td></tr>
+<tr><td width="25%"><a href="drfit.html">drfit</a></td>
+<td>Fit dose-response models</td></tr>
+<tr><td width="25%"><a href="drplot.html">drplot</a></td>
+<td>Plot dose-response models</td></tr>
+</table>
+</body></html>
diff --git a/chm/Rchm.css b/chm/Rchm.css
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+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(0%, 0%, 100%);
+ font-family: monospace;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+IMG.toplogo{ vertical-align: middle }
+
diff --git a/chm/antifoul.html b/chm/antifoul.html
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+<html><head><title>Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells</title>
+<link rel="stylesheet" type="text/css" href="Rchm.css">
+</head>
+<body>
+
+<table width="100%"><tr><td>antifoul(drfit)</td><td align="right">R Documentation</td></tr></table><object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">
+<param name="keyword" value="R: antifoul">
+<param name="keyword" value=" Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells">
+</object>
+
+
+<h2>Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells</h2>
+
+
+<h3>Description</h3>
+
+<p>
+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
+</p>
+
+
+<h3>Usage</h3>
+
+<pre>data(rivers)</pre>
+
+
+<h3>Format</h3>
+
+<p>
+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.
+</p>
+
+
+<h3>Source</h3>
+
+<p>
+<a href="http://www.uft.uni-bremen.de/chemie">http://www.uft.uni-bremen.de/chemie</a>
+</p>
+
+
+
+<hr><div align="center"><a href="00Index.html">[Package Contents]</a></div>
+
+</body></html>
diff --git a/chm/drdata.html b/chm/drdata.html
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+++ b/chm/drdata.html
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+<html><head><title>Get dose-response data</title>
+<link rel="stylesheet" type="text/css" href="Rchm.css">
+</head>
+<body>
+
+<table width="100%"><tr><td>drdata(drfit)</td><td align="right">R Documentation</td></tr></table><object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">
+<param name="keyword" value="R: drdata">
+<param name="keyword" value=" Get dose-response data">
+</object>
+
+
+<h2>Get dose-response data</h2>
+
+
+<h3>Description</h3>
+
+<p>
+Get dose-response data from a remote mysql server
+</p>
+
+
+<h3>Usage</h3>
+
+<pre>
+ drdata(substances, experimentator = "%", db = "cytotox", celltype = "IPC-81",
+ whereClause = "1", ok = "'ok'")
+</pre>
+
+
+<h3>Arguments</h3>
+
+<table summary="R argblock">
+<tr valign="top"><td><code>substances</code></td>
+<td>
+A string or an array of strings with the substance names for
+which dose-response data is to be retrieved.</td></tr>
+<tr valign="top"><td><code>experimentator</code></td>
+<td>
+The name of the experimentator whose data is to be used.</td></tr>
+<tr valign="top"><td><code>db</code></td>
+<td>
+The database to be used. Currently only "cytotox" of the UFT Department of
+Bioorganic Chemistry is supported.</td></tr>
+<tr valign="top"><td><code>celltype</code></td>
+<td>
+Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are supported.</td></tr>
+<tr valign="top"><td><code>whereClause</code></td>
+<td>
+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).</td></tr>
+<tr valign="top"><td><code>ok</code></td>
+<td>
+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.</td></tr>
+</table>
+
+<h3>Details</h3>
+
+<p>
+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 &lsquo;<TT>/etc/odbcinst.ini</TT>&rsquo;
+containing:
+<table summary="Rd table">
+<tr>
+ <td align="left">[MySQL] </td> <td align="left"> </td> <td align="left"> </td>
+</tr>
+<tr>
+ <td align="left"> Description </td> <td align="left"> = </td> <td align="left"> MySQL driver for ODBC </td>
+</tr>
+<tr>
+ <td align="left"> Driver </td> <td align="left"> = </td> <td align="left"> /usr/local/lib/libmyodbc.so </td>
+</tr>
+<tr>
+ <td align="left"> Setup </td> <td align="left"> = </td> <td align="left"> /usr/lib/odbc/libodbcmyS.so </td>
+</tr>
+</table>
+<p>
+and the file &lsquo;<TT>/etc/odbc.ini</TT>&rsquo; containing:
+<table summary="Rd table">
+<tr>
+ <td align="left">[cytotox] </td> <td align="left"> </td> <td align="left"> </td>
+</tr>
+<tr>
+ <td align="left"> Description </td> <td align="left"> = </td> <td align="left"> Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen </td>
+</tr>
+<tr>
+ <td align="left"> Driver </td> <td align="left"> = </td> <td align="left"> MySQL </td>
+</tr>
+<tr>
+ <td align="left"> Trace </td> <td align="left"> = </td> <td align="left"> Yes </td>
+</tr>
+<tr>
+ <td align="left"> TraceFile </td> <td align="left"> = </td> <td align="left"> /tmp/odbc.log </td>
+</tr>
+<tr>
+ <td align="left"> Database </td> <td align="left"> = </td> <td align="left"> cytotox </td>
+</tr>
+<tr>
+ <td align="left"> Server </td> <td align="left"> = </td> <td align="left"> eckehaat </td>
+</tr>
+<tr>
+ <td align="left"> Port </td> <td align="left"> = </td> <td align="left"> 3306 </td>
+</tr>
+</table>
+.
+</p>
+
+
+<h3>Value</h3>
+
+<table summary="R argblock">
+<tr valign="top"><td><code>data</code></td>
+<td>
+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.</td></tr>
+</table>
+
+<h3>Author(s)</h3>
+
+<p>
+Johannes Ranke
+<a href="mailto:jranke@uni-bremen.de">jranke@uni-bremen.de</a>
+<a href="http://www.uft.uni-bremen.de/chemie/ranke">http://www.uft.uni-bremen.de/chemie/ranke</a>
+</p>
+
+
+<h3>Examples</h3>
+
+<pre>
+# Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81 cells
+## Not run: data &lt;- drdata(c("TBT","Zn Pyrithion"))
+</pre>
+
+
+
+<hr><div align="center"><a href="00Index.html">[Package Contents]</a></div>
+
+</body></html>
diff --git a/chm/drfit.chm b/chm/drfit.chm
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diff --git a/chm/drfit.hhp b/chm/drfit.hhp
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+[OPTIONS]
+Auto Index=Yes
+Contents file=drfit.toc
+Compatibility=1.1 or later
+Compiled file=drfit.chm
+Default topic=00Index.html
+Display compile progress=No
+Full-text search=Yes
+Full text search stop list file=..\..\..\gnuwin32\help\R.stp
+
+
+[FILES]
+00Index.html
+antifoul.html
+drdata.html
+drfit.html
+drplot.html
diff --git a/chm/drfit.html b/chm/drfit.html
new file mode 100644
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--- /dev/null
+++ b/chm/drfit.html
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+<html><head><title>Fit dose-response models</title>
+<link rel="stylesheet" type="text/css" href="Rchm.css">
+</head>
+<body>
+
+<table width="100%"><tr><td>drfit(drfit)</td><td align="right">R Documentation</td></tr></table><object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">
+<param name="keyword" value="R: drfit">
+<param name="keyword" value=" Fit dose-response models">
+</object>
+
+
+<h2>Fit dose-response models</h2>
+
+
+<h3>Description</h3>
+
+<p>
+Fit dose-response relationships to dose-response data and calculate
+biometric results for (eco)toxicity evaluation
+</p>
+
+
+<h3>Usage</h3>
+
+<pre>
+ drfit(data, startlogEC50 = NA, lognorm = TRUE, logis = FALSE,
+ linearlogis = FALSE, b0 = 2, f0 = 0)
+</pre>
+
+
+<h3>Arguments</h3>
+
+<table summary="R argblock">
+<tr valign="top"><td><code>data</code></td>
+<td>
+A data frame as returned from <code><a href="drdata.html">drdata</a></code>. 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><a href="drplot.html">drplot</a></code> function, a factor called "dosefactor" also has to be
+present, containing the dose as a factor.
+</td></tr>
+<tr valign="top"><td><code>startlogEC50</code></td>
+<td>
+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.</td></tr>
+<tr valign="top"><td><code>lognorm</code></td>
+<td>
+A boolean defining if cumulative density curves of normal distributions
+are fitted to the data. Default ist TRUE.</td></tr>
+<tr valign="top"><td><code>logis</code></td>
+<td>
+A boolean defining if cumulative densitiy curves of logistic distributions
+are fitted to the data. Default is FALSE.</td></tr>
+<tr valign="top"><td><code>linearlogis</code></td>
+<td>
+A boolean defining if the linear-logistic function as defined by van Ewijk and Hoekstra
+1993 is fitted to the data. Default is FALSE.</td></tr>
+<tr valign="top"><td><code>b0,f0</code></td>
+<td>
+If the linearlogistic model is fitted, b0 and f0 give the possibility to
+adapt the starting values for the parameters b and f.</td></tr>
+</table>
+
+<h3>Value</h3>
+
+<table summary="R argblock">
+<tr valign="top"><td><code>results</code></td>
+<td>
+A data frame containing at least one line for each substance. If the data did not
+show a mean response &lt; 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.</td></tr>
+</table>
+
+<h3>Author(s)</h3>
+
+<p>
+Johannes Ranke
+<a href="mailto:jranke@uni-bremen.de">jranke@uni-bremen.de</a>
+<a href="http://www.uft.uni-bremen.de/chemie/ranke">http://www.uft.uni-bremen.de/chemie/ranke</a>
+</p>
+
+
+<h3>Examples</h3>
+
+<pre>
+## Not run: data(antifoul)
+## Not run: r &lt;- drfit(antifoul)
+## Not run: format(r,digits=2)
+</pre>
+
+
+
+<hr><div align="center"><a href="00Index.html">[Package Contents]</a></div>
+
+</body></html>
diff --git a/chm/drfit.toc b/chm/drfit.toc
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--- /dev/null
+++ b/chm/drfit.toc
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+<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
+<HEAD></HEAD><HTML><BODY>
+<UL>
+<LI> <OBJECT type="text/sitemap">
+<param name="Name" value="Package drfit: Contents">
+<param name="Local" value="00Index.html">
+</OBJECT>
+<LI> <OBJECT type="text/sitemap">
+<param name="Name" value="Package drfit: R objects">
+</OBJECT>
+<UL>
+<LI> <OBJECT type="text/sitemap">
+<param name="Name" value="antifoul">
+<param name="Local" value="antifoul.html">
+</OBJECT>
+<LI> <OBJECT type="text/sitemap">
+<param name="Name" value="drdata">
+<param name="Local" value="drdata.html">
+</OBJECT>
+<LI> <OBJECT type="text/sitemap">
+<param name="Name" value="drfit">
+<param name="Local" value="drfit.html">
+</OBJECT>
+<LI> <OBJECT type="text/sitemap">
+<param name="Name" value="drplot">
+<param name="Local" value="drplot.html">
+</OBJECT>
+</UL>
+<LI> <OBJECT type="text/sitemap">
+<param name="Name" value="Package drfit: Titles">
+</OBJECT>
+<UL>
+<LI> <OBJECT type="text/sitemap">
+<param name="Name" value="Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells">
+<param name="Local" value="antifoul.html">
+</OBJECT>
+<LI> <OBJECT type="text/sitemap">
+<param name="Name" value="Fit dose-response models">
+<param name="Local" value="drfit.html">
+</OBJECT>
+<LI> <OBJECT type="text/sitemap">
+<param name="Name" value="Get dose-response data">
+<param name="Local" value="drdata.html">
+</OBJECT>
+<LI> <OBJECT type="text/sitemap">
+<param name="Name" value="Plot dose-response models">
+<param name="Local" value="drplot.html">
+</OBJECT>
+</UL>
+</UL>
+</BODY></HTML>
diff --git a/chm/drplot.html b/chm/drplot.html
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--- /dev/null
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+<html><head><title>Plot dose-response models</title>
+<link rel="stylesheet" type="text/css" href="Rchm.css">
+</head>
+<body>
+
+<table width="100%"><tr><td>drplot(drfit)</td><td align="right">R Documentation</td></tr></table><object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">
+<param name="keyword" value="R: drplot">
+<param name="keyword" value=" Plot dose-response models">
+</object>
+
+
+<h2>Plot dose-response models</h2>
+
+
+<h3>Description</h3>
+
+<p>
+Produce graphics of dose-response data and dose-response relationships
+either combined or separately, for one or more substances.
+</p>
+
+
+<h3>Usage</h3>
+
+<pre>
+ drplot(drresults, data, dtype, alpha, path, fileprefix, overlay,
+ postscript, color, colors, fitcolors)
+</pre>
+
+
+<h3>Arguments</h3>
+
+<table summary="R argblock">
+<tr valign="top"><td><code>drresults</code></td>
+<td>
+A data frame as returned from <code><a href="drfit.html">drfit</a></code>.
+</td></tr>
+<tr valign="top"><td><code>data</code></td>
+<td>
+A data frame as returned from <code><a href="drdata.html">drdata</a></code>. 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.
+</td></tr>
+<tr valign="top"><td><code>dtype</code></td>
+<td>
+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.
+</td></tr>
+<tr valign="top"><td><code>alpha</code></td>
+<td>
+The confidence level, defaulting to 0.95, only used if dtype "conf" has been
+chosen.
+</td></tr>
+<tr valign="top"><td><code>path</code></td>
+<td>
+The path where graphic files should be put if any are produced. Defaults
+to "./" i.e. the current working directory of R.
+</td></tr>
+<tr valign="top"><td><code>fileprefix</code></td>
+<td>
+A string which will form the beginning of each filename, if graphic files are
+created. Defaults to "drplot".
+</td></tr>
+<tr valign="top"><td><code>overlay</code></td>
+<td>
+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.
+</td></tr>
+<tr valign="top"><td><code>postscript</code></td>
+<td>
+If TRUE, (a) postscript graph(s) will be created. Otherwise, graphics will be
+displayed with a screen graphics device.
+</td></tr>
+<tr valign="top"><td><code>color</code></td>
+<td>
+If TRUE, a sensible selection of colors will be attempted. If false, everything
+will be drawn in black
+</td></tr>
+<tr valign="top"><td><code>colors</code></td>
+<td>
+This is a vector of colors, defaulting to 1:8, used for plotting the data.
+</td></tr>
+<tr valign="top"><td><code>fitcolors</code></td>
+<td>
+Here you can specify a palette for the colors of the dose-response fits. The
+default value is "default", which produces rainbow colors.
+</td></tr>
+</table>
+
+<h3>Value</h3>
+
+<table summary="R argblock">
+<tr valign="top"><td><code>results</code></td>
+<td>
+A data frame containing at least one line for each substance. If the data did not
+show a mean response &lt; 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.</td></tr>
+</table>
+
+<h3>Author(s)</h3>
+
+<p>
+Johannes Ranke
+<a href="mailto:jranke@uni-bremen.de">jranke@uni-bremen.de</a>
+<a href="http://www.uft.uni-bremen.de/chemie/ranke">http://www.uft.uni-bremen.de/chemie/ranke</a>
+</p>
+
+
+<h3>Examples</h3>
+
+<pre>
+## Not run: data(antifoul)
+## Not run: r &lt;- drfit(antifoul)
+## Not run: format(r,digits=2)
+</pre>
+
+
+
+<hr><div align="center"><a href="00Index.html">[Package Contents]</a></div>
+
+</body></html>
diff --git a/chm/logo.jpg b/chm/logo.jpg
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+++ b/chm/logo.jpg
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