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-rw-r--r--docs/reference/IM1xIPC81.html28
-rw-r--r--docs/reference/IM1xVibrio.html28
-rw-r--r--docs/reference/XY.html28
-rw-r--r--docs/reference/antifoul.html30
-rw-r--r--docs/reference/checkcontrols.html30
-rw-r--r--docs/reference/checkexperiment.html30
-rw-r--r--docs/reference/checksubstance.html30
-rw-r--r--docs/reference/drcfit.html34
-rw-r--r--docs/reference/drdata.html97
-rw-r--r--docs/reference/drfit-package-1.pngbin60443 -> 64002 bytes
-rw-r--r--docs/reference/drfit-package.html34
-rw-r--r--docs/reference/drfit.html34
-rw-r--r--docs/reference/drplot-1.pngbin0 -> 28404 bytes
-rw-r--r--docs/reference/drplot-2.pngbin0 -> 26761 bytes
-rw-r--r--docs/reference/drplot.html34
-rw-r--r--docs/reference/index.html224
-rw-r--r--docs/reference/linlogitf.html30
-rw-r--r--docs/reference/pyrithione.html28
18 files changed, 474 insertions, 245 deletions
diff --git a/docs/reference/IM1xIPC81.html b/docs/reference/IM1xIPC81.html
index 2800440..d14afca 100644
--- a/docs/reference/IM1xIPC81.html
+++ b/docs/reference/IM1xIPC81.html
@@ -21,12 +21,15 @@
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
-
+
+
+
<meta property="og:title" content="Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells — IM1xIPC81" />
<meta property="og:description" content="This is the raw data documenting the influence of the alkyl
@@ -40,6 +43,9 @@
This is a subset (only the BF4 anion) of the data
shown in Figure 3 in Ranke et al. (2004)." />
<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -62,8 +68,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">drfit</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">drfit</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -80,6 +90,7 @@
<ul class="nav navbar-nav navbar-right">
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -87,12 +98,15 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells</h1>
+
+ <div class="hidden name"><code>IM1xIPC81.Rd</code></div>
</div>
+ <div class="ref-description">
<p>This is the raw data documenting the influence of the alkyl
chain length in 3 position on the toxicity to the
@@ -105,6 +119,7 @@
This is a subset (only the BF4 anion) of the data
shown in Figure 3 in Ranke et al. (2004).</p>
+ </div>
<pre class="usage"><span class='fu'>data</span>(<span class='no'>IM1xIPC81</span>)</pre>
@@ -214,5 +229,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/IM1xVibrio.html b/docs/reference/IM1xVibrio.html
index 22ab40e..594efe1 100644
--- a/docs/reference/IM1xVibrio.html
+++ b/docs/reference/IM1xVibrio.html
@@ -21,12 +21,15 @@
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
-
+
+
+
<meta property="og:title" content="Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri — IM1xVibrio" />
<meta property="og:description" content="This is the raw data documenting the influence of the alkyl chain length in 3
@@ -37,6 +40,9 @@
IM14 BF4 means 1-methyl-3-butylimidazolium tetrafluoroborate and
IM1-10 BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate." />
<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -59,8 +65,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">drfit</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">drfit</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -77,6 +87,7 @@
<ul class="nav navbar-nav navbar-right">
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -84,12 +95,15 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri</h1>
+
+ <div class="hidden name"><code>IM1xVibrio.Rd</code></div>
</div>
+ <div class="ref-description">
<p>This is the raw data documenting the influence of the alkyl chain length in 3
position on the toxicity to the marine luminescent bacteria <em>V.
@@ -99,6 +113,7 @@
IM14 BF4 means 1-methyl-3-butylimidazolium tetrafluoroborate and
IM1-10 BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate.</p>
+ </div>
<pre class="usage"><span class='fu'>data</span>(<span class='no'>IM1xVibrio</span>)</pre>
@@ -248,5 +263,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/XY.html b/docs/reference/XY.html
index 47ef324..2af3026 100644
--- a/docs/reference/XY.html
+++ b/docs/reference/XY.html
@@ -21,17 +21,23 @@
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
-
+
+
+
<meta property="og:title" content="Dose-Response data for two substances X and Y — XY" />
<meta property="og:description" content="This is just a sample Lemna growth rate data set for two substances
arbitrarily named X and Y." />
<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -54,8 +60,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">drfit</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">drfit</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -72,6 +82,7 @@
<ul class="nav navbar-nav navbar-right">
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -79,16 +90,20 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Dose-Response data for two substances X and Y</h1>
+
+ <div class="hidden name"><code>XY.Rd</code></div>
</div>
+ <div class="ref-description">
<p>This is just a sample Lemna growth rate data set for two substances
arbitrarily named X and Y.</p>
+ </div>
<pre class="usage"><span class='fu'>data</span>(<span class='no'>XY</span>)</pre>
@@ -133,5 +148,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/antifoul.html b/docs/reference/antifoul.html
index 8dd00c9..d166ebd 100644
--- a/docs/reference/antifoul.html
+++ b/docs/reference/antifoul.html
@@ -21,19 +21,25 @@
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
-
+
+
+
<meta property="og:title" content="Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells — antifoul" />
<meta property="og:description" content="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
+ from the &quot;cytotox&quot; database of the UFT Department of Bioorganic Chemistry on
February 25, 2004" />
<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -56,8 +62,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">drfit</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">drfit</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -74,6 +84,7 @@
<ul class="nav navbar-nav navbar-right">
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -81,18 +92,22 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells</h1>
+
+ <div class="hidden name"><code>antifoul.Rd</code></div>
</div>
+ <div class="ref-description">
<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>
+ </div>
<pre class="usage"><span class='fu'>data</span>(<span class='no'>antifoul</span>)</pre>
@@ -199,5 +214,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/checkcontrols.html b/docs/reference/checkcontrols.html
index 2ab3e4d..d3e4314 100644
--- a/docs/reference/checkcontrols.html
+++ b/docs/reference/checkcontrols.html
@@ -21,17 +21,23 @@
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
-
+
+
+
<meta property="og:title" content="Check raw data from range of plates or experiments — checkcontrols" />
<meta property="og:description" content="Report control data from a specified range of microtiter plates or
experiments from a specified database." />
<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -54,8 +60,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">drfit</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">drfit</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -72,6 +82,7 @@
<ul class="nav navbar-nav navbar-right">
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -79,23 +90,27 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Check raw data from range of plates or experiments</h1>
+
+ <div class="hidden name"><code>checkcontrols.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Report control data from a specified range of microtiter plates or
experiments from a specified database.</p>
+ </div>
<pre class="usage"><span class='fu'>checkcontrols</span>(<span class='kw'>last</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"cytotox"</span>,
<span class='kw'>celltype</span> <span class='kw'>=</span> <span class='st'>"IPC-81"</span>, <span class='kw'>enzymetype</span> <span class='kw'>=</span> <span class='st'>"AChE"</span>,
<span class='kw'>organism</span> <span class='kw'>=</span> <span class='st'>"Vibrio fischeri"</span>,
<span class='kw'>endpoint</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>qcc</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"R"</span>, <span class='st'>"xbar"</span>))</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -182,5 +197,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/checkexperiment.html b/docs/reference/checkexperiment.html
index 3ec5a09..0712cd4 100644
--- a/docs/reference/checkexperiment.html
+++ b/docs/reference/checkexperiment.html
@@ -21,17 +21,23 @@
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
-
+
+
+
<meta property="og:title" content="Check raw data from a specified experiment or microtiter plate — checkexperiment" />
<meta property="og:description" content="Report metadata from a specified experiment or microtiter plate from a
specified database, box plot controls, and plot the dose-response data." />
<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -54,8 +60,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">drfit</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">drfit</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -72,6 +82,7 @@
<ul class="nav navbar-nav navbar-right">
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -79,21 +90,25 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Check raw data from a specified experiment or microtiter plate</h1>
+
+ <div class="hidden name"><code>checkexperiment.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Report metadata from a specified experiment or microtiter plate from a
specified database, box plot controls, and plot the dose-response data.</p>
+ </div>
<pre class="usage"><span class='fu'>checkplate</span>(<span class='no'>id</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"cytotox"</span>)
<span class='fu'>checkexperiment</span>(<span class='no'>id</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"ecotox"</span>, <span class='kw'>endpoint</span> <span class='kw'>=</span> <span class='st'>"%"</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -155,5 +170,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/checksubstance.html b/docs/reference/checksubstance.html
index 184a757..3f07df2 100644
--- a/docs/reference/checksubstance.html
+++ b/docs/reference/checksubstance.html
@@ -21,17 +21,23 @@
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
-
+
+
+
<meta property="og:title" content="Check raw data for a specified substance — checksubstance" />
<meta property="og:description" content="Report metadata for a specified substance from a specified database, and plot
the data." />
<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -54,8 +60,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">drfit</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">drfit</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -72,6 +82,7 @@
<ul class="nav navbar-nav navbar-right">
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -79,23 +90,27 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Check raw data for a specified substance</h1>
+
+ <div class="hidden name"><code>checksubstance.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Report metadata for a specified substance from a specified database, and plot
the data.</p>
+ </div>
<pre class="usage"><span class='fu'>checksubstance</span>(<span class='no'>substance</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"cytotox"</span>, <span class='kw'>experimentator</span> <span class='kw'>=</span> <span class='st'>"%"</span>,
<span class='kw'>celltype</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>enzymetype</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>organism</span> <span class='kw'>=</span> <span class='st'>"%"</span>,
<span class='kw'>endpoint</span> <span class='kw'>=</span> <span class='st'>"%"</span>,
<span class='kw'>whereClause</span> <span class='kw'>=</span> <span class='st'>"1"</span>, <span class='kw'>ok</span> <span class='kw'>=</span> <span class='st'>"%"</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -189,5 +204,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/drcfit.html b/docs/reference/drcfit.html
index b208f4b..d08b4b0 100644
--- a/docs/reference/drcfit.html
+++ b/docs/reference/drcfit.html
@@ -21,17 +21,23 @@
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
-
+
+
+
<meta property="og:title" content="Fit dose-response models using the drc package — drcfit" />
<meta property="og:description" content="Fit dose-response relationships to dose-response data and calculate
biometric results for (eco)toxicity evaluation using the drc package" />
<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -54,8 +60,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">drfit</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">drfit</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -72,6 +82,7 @@
<ul class="nav navbar-nav navbar-right">
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -79,22 +90,26 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Fit dose-response models using the drc package</h1>
+
+ <div class="hidden name"><code>drcfit.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Fit dose-response relationships to dose-response data and calculate
biometric results for (eco)toxicity evaluation using the drc package</p>
+ </div>
<pre class="usage"><span class='fu'>drcfit</span>(<span class='no'>data</span>, <span class='kw'>chooseone</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>probit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>logit</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>weibull</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>linlogit</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0.95</span>,
<span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -215,9 +230,9 @@
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
- <p>Further examples are given in help pages to the datasets
+ <div class='dont-index'><p>Further examples are given in help pages to the datasets
<code>antifoul</code>, <code>IM1xIPC81</code> and
- <code>IM1xVibrio</code>.</p>
+ <code>IM1xVibrio</code>.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
@@ -270,5 +285,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/drdata.html b/docs/reference/drdata.html
index 6387e76..fc962be 100644
--- a/docs/reference/drdata.html
+++ b/docs/reference/drdata.html
@@ -21,16 +21,22 @@
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
-
+
+
+
<meta property="og:title" content="Get dose-response data via RODBC — drdata" />
<meta property="og:description" content="Get dose-response data from an adequate ODBC data source" />
<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -53,8 +59,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">drfit</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">drfit</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -71,6 +81,7 @@
<ul class="nav navbar-nav navbar-right">
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -78,21 +89,25 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Get dose-response data via RODBC</h1>
+
+ <div class="hidden name"><code>drdata.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Get dose-response data from an adequate ODBC data source</p>
+ </div>
<pre class="usage"><span class='fu'>drdata</span>(<span class='no'>substances</span>, <span class='kw'>experimentator</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"cytotox"</span>, <span class='kw'>celltype</span> <span class='kw'>=</span> <span class='st'>"IPC-81"</span>,
<span class='kw'>enzymetype</span><span class='kw'>=</span><span class='st'>"AChE"</span>, <span class='kw'>organism</span><span class='kw'>=</span><span class='st'>"Vibrio fischeri"</span>, <span class='kw'>endpoint</span><span class='kw'>=</span><span class='st'>"Luminescence"</span>,
<span class='kw'>whereClause</span> <span class='kw'>=</span> <span class='st'>"1"</span>, <span class='kw'>ok</span> <span class='kw'>=</span> <span class='st'>"'ok','no fit'"</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -165,55 +180,24 @@
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 <code class="file">/etc/odbcinst.ini</code>
- containing:</p><table><tr><td>
- [MySQL] </td>
-<td> </td>
-<td> </td>
-</tr><tr><td>
- Description </td>
-<td> = </td>
-<td> MySQL driver for ODBC </td>
-</tr><tr><td>
- Driver </td>
-<td> = </td>
-<td> /usr/local/lib/libmyodbc.so </td>
-</tr><tr><td>
- Setup </td>
-<td> = </td>
-<td> /usr/lib/odbc/libodbcmyS.so </td>
-</tr></table><p>and the file <code class="file">/etc/odbc.ini</code> containing:</p><table><tr><td>
- [cytotox] </td>
-<td> </td>
-<td> </td>
-</tr><tr><td>
- Description </td>
-<td> = </td>
-<td> Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen </td>
-</tr><tr><td>
- Driver </td>
-<td> = </td>
-<td> MySQL </td>
-</tr><tr><td>
- Trace </td>
-<td> = </td>
-<td> Yes </td>
-</tr><tr><td>
- TraceFile </td>
-<td> = </td>
-<td> /tmp/odbc.log </td>
-</tr><tr><td>
- Database </td>
-<td> = </td>
-<td> cytotox </td>
-</tr><tr><td>
- Server </td>
-<td> = </td>
-<td> eckehaat </td>
-</tr><tr><td>
- Port </td>
-<td> = </td>
-<td> 3306 </td>
-</tr></table>
+ containing:</p><table class='table'>
+<tr><td>[MySQL]</td><td></td><td></td></tr>
+<tr><td>Description</td><td>=</td><td>MySQL driver for ODBC</td></tr>
+<tr><td>Driver</td><td>=</td><td>/usr/local/lib/libmyodbc.so</td></tr>
+<tr><td>Setup</td><td>=</td><td>/usr/lib/odbc/libodbcmyS.so</td></tr>
+<tr><td></td><td>[MySQL]</td><td></td></tr>
+</table>
+<p>and the file <code class="file">/etc/odbc.ini</code> containing:</p><table class='table'>
+<tr><td>[cytotox]</td><td></td><td></td></tr>
+<tr><td>Description</td><td>=</td><td>Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen</td></tr>
+<tr><td>Driver</td><td>=</td><td>MySQL</td></tr>
+<tr><td>Trace</td><td>=</td><td>Yes</td></tr>
+<tr><td>TraceFile</td><td>=</td><td>/tmp/odbc.log</td></tr>
+<tr><td>Database</td><td>=</td><td>cytotox</td></tr>
+<tr><td>Server</td><td>=</td><td>eckehaat</td></tr>
+<tr><td>Port</td><td>=</td><td>3306</td></tr>
+<tr><td></td><td>[cytotox]</td><td></td></tr>
+</table>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
@@ -256,5 +240,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/drfit-package-1.png b/docs/reference/drfit-package-1.png
index 64d831f..62e80fb 100644
--- a/docs/reference/drfit-package-1.png
+++ b/docs/reference/drfit-package-1.png
Binary files differ
diff --git a/docs/reference/drfit-package.html b/docs/reference/drfit-package.html
index 1ce4fed..d2aa326 100644
--- a/docs/reference/drfit-package.html
+++ b/docs/reference/drfit-package.html
@@ -21,16 +21,22 @@
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
-
+
+
+
<meta property="og:title" content="Dose-response data evaluation — drfit-package" />
<meta property="og:description" content="See ../DESCRIPTION" />
<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -53,8 +59,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">drfit</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">drfit</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -71,6 +81,7 @@
<ul class="nav navbar-nav navbar-right">
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -78,15 +89,19 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Dose-response data evaluation</h1>
+
+ <div class="hidden name"><code>drfit-package.Rd</code></div>
</div>
+ <div class="ref-description">
<p>See <a href='../DESCRIPTION'>../DESCRIPTION</a></p>
+ </div>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
@@ -102,9 +117,9 @@ of R for chemists.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
- <p>On CRAN, there is another, more statistically sophisticated package with
+ <div class='dont-index'><p>On CRAN, there is another, more statistically sophisticated package with
similar functionality called <code>drc</code>. I think the advantage of my package
-is its user-friendliness.</p>
+is its user-friendliness.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
@@ -116,7 +131,7 @@ is its user-friendliness.</p>
#&gt; 2 Zn Pyrithion 27 81 -2.1 2.0 probit -0.40 -0.51 -0.292 microM 0.23 -0.40
#&gt; b
#&gt; 1 0.68
-#&gt; 2 0.42</div><div class='input'><span class='fu'>drplot</span>(<span class='no'>r</span>,<span class='no'>antifoul</span>,<span class='kw'>overlay</span><span class='kw'>=</span><span class='fl'>TRUE</span>,<span class='kw'>bw</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='img'><img src='drfit-package-1.png' alt='' width='700' height='432.632880098887' /></div></pre>
+#&gt; 2 0.42</div><div class='input'><span class='fu'>drplot</span>(<span class='no'>r</span>,<span class='no'>antifoul</span>,<span class='kw'>overlay</span><span class='kw'>=</span><span class='fl'>TRUE</span>,<span class='kw'>bw</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='img'><img src='drfit-package-1.png' alt='' width='700' height='433' /></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -150,5 +165,8 @@ Author and Maintainer: Johannes Ranke &lt;jranke@uni-bremen.de&gt;
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/drfit.html b/docs/reference/drfit.html
index 4430a5b..4aa7935 100644
--- a/docs/reference/drfit.html
+++ b/docs/reference/drfit.html
@@ -21,17 +21,23 @@
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
-
+
+
+
<meta property="og:title" content="Fit dose-response models — drfit" />
<meta property="og:description" content="Fit dose-response relationships to dose-response data and calculate
biometric results for (eco)toxicity evaluation" />
<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -54,8 +60,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">drfit</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">drfit</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -72,6 +82,7 @@
<ul class="nav navbar-nav navbar-right">
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -79,16 +90,20 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Fit dose-response models</h1>
+
+ <div class="hidden name"><code>drfit.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Fit dose-response relationships to dose-response data and calculate
biometric results for (eco)toxicity evaluation</p>
+ </div>
<pre class="usage"><span class='fu'>drfit</span>(<span class='no'>data</span>, <span class='kw'>startlogED50</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>chooseone</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>probit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>logit</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>weibull</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>linlogit</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0.95</span>, <span class='kw'>linlogitWrong</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
@@ -96,7 +111,7 @@
<span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>EDx</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>EDx.tolerance</span> <span class='kw'>=</span> <span class='fl'>1e-4</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -255,12 +270,12 @@
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
- <p>Further examples are given in help pages to the datasets
+ <div class='dont-index'><p>Further examples are given in help pages to the datasets
<code>antifoul</code>, <code>IM1xIPC81</code> and
<code>IM1xVibrio</code>.
Since version 0.6.1 of this package, there is a drop-in replacement function
<code>drcfit</code> which internally uses the drc package and also gives
- confidence intervals for EDx values via this package.</p>
+ confidence intervals for EDx values via this package.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
@@ -309,5 +324,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/drplot-1.png b/docs/reference/drplot-1.png
new file mode 100644
index 0000000..bcddcd1
--- /dev/null
+++ b/docs/reference/drplot-1.png
Binary files differ
diff --git a/docs/reference/drplot-2.png b/docs/reference/drplot-2.png
new file mode 100644
index 0000000..75a75af
--- /dev/null
+++ b/docs/reference/drplot-2.png
Binary files differ
diff --git a/docs/reference/drplot.html b/docs/reference/drplot.html
index b64d4e5..e5cbb22 100644
--- a/docs/reference/drplot.html
+++ b/docs/reference/drplot.html
@@ -21,17 +21,23 @@
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
-
+
+
+
<meta property="og:title" content="Plot dose-response models — drplot" />
<meta property="og:description" content="Produce graphics of dose-response data and dose-response relationships
either combined or separately, for one or more substances." />
<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -54,8 +60,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">drfit</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">drfit</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -72,6 +82,7 @@
<ul class="nav navbar-nav navbar-right">
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -79,22 +90,26 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Plot dose-response models</h1>
+
+ <div class="hidden name"><code>drplot.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Produce graphics of dose-response data and dose-response relationships
either combined or separately, for one or more substances.</p>
+ </div>
<pre class="usage"><span class='fu'>drplot</span>(<span class='no'>drresults</span>, <span class='no'>data</span>, <span class='no'>dtype</span>, <span class='no'>alpha</span>, <span class='no'>ctype</span>, <span class='no'>path</span>,
<span class='no'>fileprefix</span>, <span class='no'>overlay</span>, <span class='no'>xlim</span>, <span class='no'>ylim</span>, <span class='no'>xlab</span>, <span class='no'>ylab</span>, <span class='no'>axes</span>, <span class='no'>frame.plot</span>, <span class='no'>postscript</span>,
<span class='no'>pdf</span>, <span class='no'>png</span>, <span class='no'>bw</span>, <span class='no'>pointsize</span>, <span class='no'>colors</span>, <span class='no'>ltys</span>, <span class='no'>pchs</span>, <span class='no'>devoff</span>, <span class='no'>lpos</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -243,9 +258,7 @@
<pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>antifoul</span>)
<span class='no'>r</span> <span class='kw'>&lt;-</span> <span class='fu'>drfit</span>(<span class='no'>antifoul</span>)</div><div class='output co'>#&gt; <span class='message'></span>
#&gt; <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'></span>
-#&gt; <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><span class='co'># NOT RUN {</span>
-<span class='fu'>drplot</span>(<span class='no'>r</span>,<span class='no'>antifoul</span>)
-<span class='co'># }</span></pre>
+#&gt; <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='input'><span class='fu'>drplot</span>(<span class='no'>r</span>,<span class='no'>antifoul</span>)</div><div class='img'><img src='drplot-1.png' alt='' width='700' height='433' /></div><div class='img'><img src='drplot-2.png' alt='' width='700' height='433' /></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -280,5 +293,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/index.html b/docs/reference/index.html
index e3ecd24..2b1f884 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -21,13 +21,19 @@
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
-
+
+
+
<meta property="og:title" content="Function reference" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -50,8 +56,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">drfit</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">drfit</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -68,6 +78,7 @@
<ul class="nav navbar-nav navbar-right">
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -75,112 +86,108 @@
</header>
- <div class="row">
- <div class="col-md-9">
+<div class="row">
+ <div class="contents col-md-9">
<div class="page-header">
- <h1>
- Reference
- <small>version&nbsp;0.7.1</small>
- </h1>
+ <h1>Reference</h1>
</div>
- <div class="contents">
- <table class="ref-index">
-
- <colgroup>
- <col class="alias" />
- <col class="title" />
- </colgroup>
-
- <tbody>
- <tr>
- <th colspan="2">
- <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
- <p class="section-desc"></p>
- </th>
- </tr>
- <tr>
- <!-- -->
- <td>
- <p><code><a href="antifoul.html">data</a></code> </p>
- </td>
- <td><p>Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="checkcontrols.html">checkcontrols</a></code> </p>
- </td>
- <td><p>Check raw data from range of plates or experiments</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="checkexperiment.html">checkplate</a></code> <code><a href="checkexperiment.html">checkexperiment</a></code> </p>
- </td>
- <td><p>Check raw data from a specified experiment or microtiter plate</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="drcfit.html">drcfit</a></code> </p>
- </td>
- <td><p>Fit dose-response models using the drc package</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="drdata.html">drdata</a></code> </p>
- </td>
- <td><p>Get dose-response data via RODBC</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="drfit-package.html">drfit-package</a></code> </p>
- </td>
- <td><p>Dose-response data evaluation</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="drfit.html">drfit</a></code> </p>
- </td>
- <td><p>Fit dose-response models</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="drplot.html">drplot</a></code> </p>
- </td>
- <td><p>Plot dose-response models</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="IM1xIPC81.html">data</a></code> </p>
- </td>
- <td><p>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="IM1xVibrio.html">data</a></code> </p>
- </td>
- <td><p>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="linlogitf.html">linlogitf</a></code> </p>
- </td>
- <td><p>Linear-logistic function</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="pyrithione.html">data</a></code> </p>
- </td>
- <td><p>Cytotoxicity data for different pyrithionates and related species</p></td>
- </tr><tr>
- <!-- -->
- <td>
- <p><code><a href="XY.html">data</a></code> </p>
- </td>
- <td><p>Dose-Response data for two substances X and Y</p></td>
- </tr>
- </tbody>
- </table>
- </div>
+ <table class="ref-index">
+
+ <colgroup>
+
+ <col class="alias" />
+ <col class="title" />
+ </colgroup>
+
+ <tbody>
+ <tr>
+ <th colspan="2">
+ <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
+ <p class="section-desc"></p>
+ </th>
+ </tr>
+ <tr>
+
+ <td>
+ <p><code><a href="IM1xIPC81.html">IM1xIPC81</a></code> </p>
+ </td>
+ <td><p>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="IM1xVibrio.html">IM1xVibrio</a></code> </p>
+ </td>
+ <td><p>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="XY.html">XY</a></code> </p>
+ </td>
+ <td><p>Dose-Response data for two substances X and Y</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="antifoul.html">antifoul</a></code> </p>
+ </td>
+ <td><p>Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="checkcontrols.html">checkcontrols()</a></code> </p>
+ </td>
+ <td><p>Check raw data from range of plates or experiments</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="checkexperiment.html">checkplate()</a></code> <code><a href="checkexperiment.html">checkexperiment()</a></code> </p>
+ </td>
+ <td><p>Check raw data from a specified experiment or microtiter plate</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="drcfit.html">drcfit()</a></code> </p>
+ </td>
+ <td><p>Fit dose-response models using the drc package</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="drdata.html">drdata()</a></code> </p>
+ </td>
+ <td><p>Get dose-response data via RODBC</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="drfit-package.html">drfit-package</a></code> </p>
+ </td>
+ <td><p>Dose-response data evaluation</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="drfit.html">drfit()</a></code> </p>
+ </td>
+ <td><p>Fit dose-response models</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="drplot.html">drplot()</a></code> </p>
+ </td>
+ <td><p>Plot dose-response models</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="linlogitf.html">linlogitf()</a></code> </p>
+ </td>
+ <td><p>Linear-logistic function</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="pyrithione.html">pyrithione</a></code> </p>
+ </td>
+ <td><p>Cytotoxicity data for different pyrithionates and related species</p></td>
+ </tr>
+ </tbody>
+ </table>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
@@ -203,5 +210,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/linlogitf.html b/docs/reference/linlogitf.html
index deed92a..1dddf50 100644
--- a/docs/reference/linlogitf.html
+++ b/docs/reference/linlogitf.html
@@ -21,17 +21,23 @@
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
-
+
+
+
<meta property="og:title" content="Linear-logistic function — linlogitf" />
<meta property="og:description" content="Helper function describing a special type of dose-response curves, showing a stimulus
at subtoxic doses." />
<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -54,8 +60,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">drfit</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">drfit</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -72,6 +82,7 @@
<ul class="nav navbar-nav navbar-right">
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -79,20 +90,24 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Linear-logistic function</h1>
+
+ <div class="hidden name"><code>linlogitf.Rd</code></div>
</div>
+ <div class="ref-description">
<p>Helper function describing a special type of dose-response curves, showing a stimulus
at subtoxic doses.</p>
+ </div>
<pre class="usage"><span class='fu'>linlogitf</span>(<span class='no'>x</span>,<span class='no'>k</span>,<span class='no'>f</span>,<span class='no'>mu</span>,<span class='no'>b</span>)</pre>
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
@@ -159,5 +174,8 @@
</footer>
</div>
+
+
</body>
</html>
+
diff --git a/docs/reference/pyrithione.html b/docs/reference/pyrithione.html
index d7b6ced..1488ecb 100644
--- a/docs/reference/pyrithione.html
+++ b/docs/reference/pyrithione.html
@@ -21,18 +21,24 @@
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
-
-
+
+
+
<meta property="og:title" content="Cytotoxicity data for different pyrithionates and related species — pyrithione" />
<meta property="og:description" content="This data shows the cytotoxicity of pyrithione salts as well as the free
pyrithione, its oxidation product and some other related compounds to the
IPC-81 cell line." />
<meta name="twitter:card" content="summary" />
+
+
+
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
@@ -55,8 +61,12 @@
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
- <a class="navbar-brand" href="../index.html">drfit</a>
+ <span class="navbar-brand">
+ <a class="navbar-link" href="../index.html">drfit</a>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span>
+ </span>
</div>
+
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
@@ -73,6 +83,7 @@
<ul class="nav navbar-nav navbar-right">
</ul>
+
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
@@ -80,17 +91,21 @@
</header>
- <div class="row">
+<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Cytotoxicity data for different pyrithionates and related species</h1>
+
+ <div class="hidden name"><code>pyrithione.Rd</code></div>
</div>
+ <div class="ref-description">
<p>This data shows the cytotoxicity of pyrithione salts as well as the free
pyrithione, its oxidation product and some other related compounds to the
IPC-81 cell line.</p>
+ </div>
<pre class="usage"><span class='fu'>data</span>(<span class='no'>pyrithione</span>)</pre>
@@ -138,5 +153,8 @@
</footer>
</div>
+
+
</body>
</html>
+

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