Static documentation rebuilt by pkgdown::build_site()

20 files changed, 88 insertions, 74 deletions

diff --git a/check.log b/check.log
index b1eb3aa..2c02dfa 100644
--- a/check.log
+++ b/check.log
@@ -1,15 +1,13 @@
 * using log directory ‘/home/jranke/git/drfit/drfit.Rcheck’
-* using R version 3.4.0 (2017-04-21)
+* using R version 3.4.1 (2017-06-30)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * using session charset: UTF-8
 * using option ‘--as-cran’
 * checking for file ‘drfit/DESCRIPTION’ ... OK
 * this is package ‘drfit’ version ‘0.7.1’
 * package encoding: UTF-8
-* checking CRAN incoming feasibility ... NOTE
+* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
 Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
-
-The Date field is over a month old.
 * checking package namespace information ... OK
 * checking package dependencies ... OK
 * checking if this is a source package ... OK
@@ -71,9 +69,5 @@ The Date field is over a month old.
 * checking PDF version of manual ... OK
 * DONE
 
-Status: 1 NOTE
-See
-  ‘/home/jranke/git/drfit/drfit.Rcheck/00check.log’
-for details.
-
+Status: OK
 
diff --git a/docs/authors.html b/docs/authors.html
index 3db937a..f5e3a8f 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -25,7 +25,7 @@
 <script src="pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
diff --git a/docs/index.html b/docs/index.html
index 6360f04..c29a291 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -9,7 +9,7 @@
 <!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
 <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 <!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><!-- mathjax --><script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
+<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]-->
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
index e704e06..9c437c7 100644
--- a/docs/pkgdown.css
+++ b/docs/pkgdown.css
@@ -36,11 +36,8 @@ img.icon {
 
 /* Section anchors ---------------------------------*/
 
-.hasAnchor {
-  margin-left: -30px;
-}
-
 a.anchor {
+  margin-left: -30px;
   display:inline-block;
   width: 30px;
   height: 30px;
@@ -56,6 +53,13 @@ a.anchor {
   visibility: visible;
 }
 
+@media (max-width: 767px) {
+  .hasAnchor:hover a.anchor {
+    visibility: hidden;
+  }
+}
+
+
 /* Fixes for fixed navbar --------------------------*/
 
 .contents h1, .contents h2, .contents h3, .contents h4 {
@@ -63,6 +67,17 @@ a.anchor {
   margin-top: -60px;
 }
 
+/* Static header placement on mobile devices */
+@media (max-width: 767px) {
+  .navbar-fixed-top {
+    position: absolute;
+  }
+  .navbar {
+    padding: 0;
+  }
+}
+
+
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -107,31 +122,33 @@ table {
 
 /* Syntax highlighting ---------------------------------------------------- */
 
-code {
-  background-color: #f7f7f7;
-  color: #333;
+pre {
+  word-wrap: normal;
+  word-break: normal;
+  border: 1px solid #eee;
 }
-code a {
-  color: #375f84;
-}
-
-.warning { color: red; }
-.message { font-weight: bolder; }
-.error   { color: red; font-weight: bolder; }
 
-.fl,.number {color:rgb(21,20,181);}
-.fu,.functioncall {color:#264D66 ;}
-.ch,.st,.string {color:#375D81 ;}
-.kw,.keyword {color:black;}
-.argument {color:#264D66 ;}
-.co,.comment {color: #777;}
-.formalargs {color: #264D66;}
-.eqformalargs {color:#264D66;}
-.slot {font-style:italic;}
-.symbol {color:black ;}
-.prompt {color:black ;}
+pre, code {
+  background-color: #f8f8f8;
+  color: #333;
+}
 
 pre img {
   background-color: #fff;
   display: block;
 }
+
+code a, pre a {
+  color: #375f84;
+}
+
+.fl      {color: #1514b5;}
+.fu      {color: #000000;} /* function */
+.ch,.st  {color: #036a07;} /* string */
+.kw      {color: #264D66;} /* keyword */
+.co      {color: #888888;} /* comment */
+
+.message { color: black;   font-weight: bolder;}
+.error   { color: orange;  font-weight: bolder;}
+.warning { color: #6A0366; font-weight: bolder;}
+
diff --git a/docs/reference/IM1xIPC81.html b/docs/reference/IM1xIPC81.html
index 6ab98e7..6fe9bec 100644
--- a/docs/reference/IM1xIPC81.html
+++ b/docs/reference/IM1xIPC81.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -84,7 +84,7 @@
   shown in Figure 3 in Ranke et al. (2004).</p>
     
 
-    <pre><span class='fu'>data</span>(<span class='no'>IM1xIPC81</span>)</pre>
+    <pre class="usage"><span class='fu'>data</span>(<span class='no'>IM1xIPC81</span>)</pre>
         
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
diff --git a/docs/reference/IM1xVibrio.html b/docs/reference/IM1xVibrio.html
index 79c3d95..9cee125 100644
--- a/docs/reference/IM1xVibrio.html
+++ b/docs/reference/IM1xVibrio.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -81,7 +81,7 @@
   IM1-10 BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate.</p>
     
 
-    <pre><span class='fu'>data</span>(<span class='no'>IM1xVibrio</span>)</pre>
+    <pre class="usage"><span class='fu'>data</span>(<span class='no'>IM1xVibrio</span>)</pre>
         
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
diff --git a/docs/reference/XY.html b/docs/reference/XY.html
index a585270..7449f66 100644
--- a/docs/reference/XY.html
+++ b/docs/reference/XY.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -76,7 +76,7 @@
   arbitrarily named X and Y.</p>
     
 
-    <pre><span class='fu'>data</span>(<span class='no'>XY</span>)</pre>
+    <pre class="usage"><span class='fu'>data</span>(<span class='no'>XY</span>)</pre>
         
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
diff --git a/docs/reference/antifoul.html b/docs/reference/antifoul.html
index 92fd8e8..9beb79f 100644
--- a/docs/reference/antifoul.html
+++ b/docs/reference/antifoul.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -78,7 +78,7 @@
   February 25, 2004</p>
     
 
-    <pre><span class='fu'>data</span>(<span class='no'>antifoul</span>)</pre>
+    <pre class="usage"><span class='fu'>data</span>(<span class='no'>antifoul</span>)</pre>
         
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
diff --git a/docs/reference/checkcontrols.html b/docs/reference/checkcontrols.html
index 0e89c93..c33f7f2 100644
--- a/docs/reference/checkcontrols.html
+++ b/docs/reference/checkcontrols.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -76,7 +76,7 @@
   experiments from a specified database.</p>
     
 
-    <pre><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>,
+    <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>
diff --git a/docs/reference/checkexperiment.html b/docs/reference/checkexperiment.html
index 277bfd5..8056a56 100644
--- a/docs/reference/checkexperiment.html
+++ b/docs/reference/checkexperiment.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -76,7 +76,7 @@
   specified database, box plot controls, and plot the dose-response data.</p>
     
 
-    <pre><span class='fu'>checkplate</span>(<span class='no'>id</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"cytotox"</span>)
+    <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>
diff --git a/docs/reference/checksubstance.html b/docs/reference/checksubstance.html
index 60ae6e3..4188b19 100644
--- a/docs/reference/checksubstance.html
+++ b/docs/reference/checksubstance.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -76,7 +76,7 @@
   the data.</p>
     
 
-    <pre><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>,
+    <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>
@@ -86,7 +86,8 @@
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>substance</th>
-      <td><p>The name of the substance identifying it within the database.</p></td>
+      <td><p>The name of the substance identifying it within the database. Matching is not 
+    case-sensitive.</p></td>
     </tr>
     <tr>
       <th>db</th>
diff --git a/docs/reference/drcfit.html b/docs/reference/drcfit.html
index e7de303..d433c41 100644
--- a/docs/reference/drcfit.html
+++ b/docs/reference/drcfit.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -76,7 +76,7 @@
   biometric results for (eco)toxicity evaluation using the drc package</p>
     
 
-    <pre><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>,
+    <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>
     
diff --git a/docs/reference/drdata.html b/docs/reference/drdata.html
index dd5be7b..f4716f1 100644
--- a/docs/reference/drdata.html
+++ b/docs/reference/drdata.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -75,7 +75,7 @@
     <p>Get dose-response data from an adequate ODBC data source</p>
     
 
-    <pre><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>,
+    <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>
     
@@ -85,7 +85,7 @@
     <tr>
       <th>substances</th>
       <td><p>A string or an array of strings with the substance names for
-    which dose-response data is to be retrieved.</p></td>
+    which dose-response data is to be retrieved. Matching is case-sensitive.</p></td>
     </tr>
     <tr>
       <th>experimentator</th>
diff --git a/docs/reference/drfit-package-9.png b/docs/reference/drfit-package-9.png
index 1095620..976b68f 100644
--- a/docs/reference/drfit-package-9.png
+++ b/docs/reference/drfit-package-9.png
diff --git a/docs/reference/drfit-package.html b/docs/reference/drfit-package.html
index 17611e7..9cc3de4 100644
--- a/docs/reference/drfit-package.html
+++ b/docs/reference/drfit-package.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
diff --git a/docs/reference/drfit.html b/docs/reference/drfit.html
index 2de949f..52ecb2b 100644
--- a/docs/reference/drfit.html
+++ b/docs/reference/drfit.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -76,7 +76,7 @@
   biometric results for (eco)toxicity evaluation</p>
     
 
-    <pre><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>,
+    <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>,
   <span class='kw'>allWrong</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>ps0</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>ls0</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>ws0</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>b0</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>f0</span> <span class='kw'>=</span> <span class='fl'>0</span>,
   <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
diff --git a/docs/reference/drplot.html b/docs/reference/drplot.html
index 9a678e1..4225966 100644
--- a/docs/reference/drplot.html
+++ b/docs/reference/drplot.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -76,7 +76,7 @@
   either combined or separately, for one or more substances.</p>
     
 
-    <pre><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>,
+    <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>
     
diff --git a/docs/reference/index.html b/docs/reference/index.html
index d92d4dc..896e64d 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -68,8 +68,10 @@
       <div class="row">
   <div class="col-md-9">
     <div class="page-header">
-      <h1>Function reference</h1>
-      <h4>version&nbsp;0.7.1</h4>
+      <h1>
+        Reference
+        <small>version&nbsp;0.7.1</small>
+      </h1>
     </div>
 
     <div class="contents">
@@ -90,7 +92,7 @@
         <tr>
           <!--  -->
           <td>
-            <p><code><a href="antifoul.html">antifoul</a></code> </p>
+            <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>
@@ -102,7 +104,7 @@
         </tr><tr>
           <!--  -->
           <td>
-            <p><code><a href="checkexperiment.html">checkexperiment</a></code> <code><a href="checkexperiment.html">checkplate</a></code> </p>
+            <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>
@@ -138,13 +140,13 @@
         </tr><tr>
           <!--  -->
           <td>
-            <p><code><a href="IM1xIPC81.html">IM1xIPC81</a></code> </p>
+            <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">IM1xVibrio</a></code> </p>
+            <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>
@@ -156,13 +158,13 @@
         </tr><tr>
           <!--  -->
           <td>
-            <p><code><a href="pyrithione.html">pyrithione</a></code> </p>
+            <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">XY</a></code> </p>
+            <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>
diff --git a/docs/reference/linlogitf.html b/docs/reference/linlogitf.html
index 8b9ba0d..b19426f 100644
--- a/docs/reference/linlogitf.html
+++ b/docs/reference/linlogitf.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -76,7 +76,7 @@
   at subtoxic doses.</p>
     
 
-    <pre><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>
+    <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>
     <table class="ref-arguments">
diff --git a/docs/reference/pyrithione.html b/docs/reference/pyrithione.html
index 7496be2..ee2cc75 100644
--- a/docs/reference/pyrithione.html
+++ b/docs/reference/pyrithione.html
@@ -25,7 +25,7 @@
 <script src="../pkgdown.js"></script>
 
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -77,7 +77,7 @@
  IPC-81 cell line.</p>
     
 
-    <pre><span class='fu'>data</span>(<span class='no'>pyrithione</span>)</pre>
+    <pre class="usage"><span class='fu'>data</span>(<span class='no'>pyrithione</span>)</pre>
         
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>