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24 files changed, 749 insertions, 514 deletions
diff --git a/docs/404.html b/docs/404.html new file mode 100644 index 0000000..e6dd347 --- /dev/null +++ b/docs/404.html @@ -0,0 +1,130 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Page not found (404) • drfit</title> + + +<!-- jquery --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + +<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> + +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> + +<!-- headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> + +<!-- pkgdown --> +<link href="pkgdown.css" rel="stylesheet"> +<script src="pkgdown.js"></script> + + + + +<meta property="og:title" content="Page not found (404)" /> + + + + +<!-- mathjax --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></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]--> + + + + </head> + + <body> + <div class="container template-title-body"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="index.html">drfit</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.3</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="index.html"> + <span class="fas fa fas fa-home fa-lg"></span> + + </a> +</li> +<li> + <a href="reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + + </ul> + + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header> + +<div class="row"> + <div class="contents col-md-9"> + <div class="page-header"> + <h1>Page not found (404)</h1> + </div> + +Content not found. Please use links in the navbar. + + </div> + +</div> + + + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + + diff --git a/docs/authors.html b/docs/authors.html index cb71793..2a8b73a 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,6 +1,6 @@ <!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html> +<html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> @@ -8,21 +8,25 @@ <title>Authors • drfit</title> + <!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" 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> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + +<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" 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"> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <!-- 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> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" 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> +<!-- headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="pkgdown.css" rel="stylesheet"> @@ -30,12 +34,15 @@ + <meta property="og:title" content="Authors" /> + <!-- mathjax --> -<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> <!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> @@ -43,6 +50,7 @@ <![endif]--> + </head> <body> @@ -51,14 +59,15 @@ <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <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">0.7.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.3</span> </span> </div> @@ -66,7 +75,7 @@ <ul class="nav navbar-nav"> <li> <a href="index.html"> - <span class="fa fa-home fa-lg"></span> + <span class="fas fa fas fa-home fa-lg"></span> </a> </li> @@ -74,7 +83,6 @@ <a href="reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -84,6 +92,7 @@ </div><!--/.navbar --> + </header> <div class="row"> @@ -94,7 +103,7 @@ <ul class="list-unstyled"> <li> - <p><strong>Johannes Ranke</strong>. Author, maintainer. <a href='https://orcid.org/0000-0003-4371-6538' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' height='16'></a> + <p><strong>Johannes Ranke</strong>. Author, maintainer. <a href='https://orcid.org/0000-0003-4371-6538' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID'></a> </p> </li> </ul> @@ -104,13 +113,14 @@ </div> + <footer> <div class="copyright"> <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> </div> </footer> @@ -118,6 +128,8 @@ + </body> </html> + diff --git a/docs/index.html b/docs/index.html index 333c303..8b78e93 100644 --- a/docs/index.html +++ b/docs/index.html @@ -1,29 +1,30 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"> <head> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <title>Dose-Response Data Evaluation • drfit</title> -<!-- 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"> -<!-- 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"> +<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous"> +<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous"> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous"> +<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"> <script src="pkgdown.js"></script><meta property="og:title" content="Dose-Response Data Evaluation"> <meta property="og:description" content="A somewhat outdated package of basic and easy-to-use functions for fitting dose-response curves to continuous dose-response data, calculating some toxicological parameters and plotting the results. Please consider using - the more powerful and actively developed 'drc' package. Functions that are + the more powerful and actively developed drc package. Functions that are fitted are the cumulative density function of the log-normal distribution - ('probit' fit), of the logistic distribution ('logit' fit), of the Weibull - distribution ('weibull' fit) and a linear-logistic model ('linlogit' fit), + (probit fit), of the logistic distribution (logit fit), of the Weibull + distribution (weibull fit) and a linear-logistic model (linlogit fit), derived from the latter, which is used to describe data showing stimulation at low doses (hormesis). In addition, functions checking, plotting and retrieving - dose-response data retrieved from a database accessed via 'odbc' are included. - As an alternative to the original fitting methods, the algorithms from the 'drc' + dose-response data retrieved from a database accessed via odbc are included. + As an alternative to the original fitting methods, the algorithms from the drc package can be used."> <meta name="twitter:card" content="summary"> -<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></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]--> @@ -33,14 +34,15 @@ <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <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">0.7.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.3</span> </span> </div> @@ -48,7 +50,7 @@ <ul class="nav navbar-nav"> <li> <a href="index.html"> - <span class="fa fa-home fa-lg"></span> + <span class="fas fa fas fa-home fa-lg"></span> </a> </li> @@ -65,24 +67,26 @@ <!--/.navbar --> + </header><div class="row"> <div class="contents col-md-9"> - <div id="drfit" class="section level1"> -<div class="page-header"><h1 class="hasAnchor"> -<a href="#drfit" class="anchor"></a>drfit</h1></div> + +<hr> +<div id="title-readme-file-for-the-drfit-r-package" class="section level2"> +<h2 class="hasAnchor"> +<a href="#title-readme-file-for-the-drfit-r-package" class="anchor"></a>title: Readme file for the drfit R package</h2> <p>Static documentation of this R package can be found at <a href="https://pkgdown.jrwb.de/drfit" class="uri">https://pkgdown.jrwb.de/drfit</a></p> </div> + </div> - <div class="col-md-3" id="sidebar"> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <div class="links"> <h2>Links</h2> <ul class="list-unstyled"> <li>Download from CRAN at <br><a href="https://cloud.r-project.org/package=drfit">https://cloud.r-project.org/package=drfit</a> </li> -<li>Report a bug at <br><a href="NA">NA</a> -</li> </ul> </div> <div class="license"> @@ -94,7 +98,7 @@ <div class="developers"> <h2>Developers</h2> <ul class="list-unstyled"> -<li>Johannes Ranke <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0003-4371-6538" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" height="16"></a> </li> +<li>Johannes Ranke <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0003-4371-6538" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID"></a> </li> </ul> </div> @@ -113,7 +117,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> </div> </footer> @@ -121,5 +125,6 @@ + </body> </html> diff --git a/docs/pkgdown.css b/docs/pkgdown.css index 6ca2f37..9145958 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -21,8 +21,6 @@ body > .container { display: flex; height: 100%; flex-direction: column; - - padding-top: 60px; } body > .container .row { @@ -58,9 +56,14 @@ img { max-width: 100%; } +/* Fix bug in bootstrap (only seen in firefox) */ +summary { + display: list-item; +} + /* Typographic tweaking ---------------------------------*/ -.contents h1.page-header { +.contents .page-header { margin-top: calc(-60px + 1em); } @@ -97,21 +100,13 @@ a.anchor { margin-top: -40px; } -/* Static header placement on mobile devices */ -@media (max-width: 767px) { - .navbar-fixed-top { - position: absolute; - } - .navbar { - padding: 0; - } -} - - /* Sidebar --------------------------*/ #sidebar { margin-top: 30px; + position: -webkit-sticky; + position: sticky; + top: 70px; } #sidebar h2 { font-size: 1.5em; @@ -128,6 +123,9 @@ a.anchor { .orcid { height: 16px; + /* margins are required by official ORCID trademark and display guidelines */ + margin-left:4px; + margin-right:4px; vertical-align: middle; } @@ -136,10 +134,9 @@ a.anchor { .ref-index th {font-weight: normal;} .ref-index td {vertical-align: top;} +.ref-index .icon {width: 40px;} .ref-index .alias {width: 40%;} -.ref-index .title {width: 60%;} - -.ref-index .alias {width: 40%;} +.ref-index-icons .alias {width: calc(40% - 40px);} .ref-index .title {width: 60%;} .ref-arguments th {text-align: right; padding-right: 10px;} @@ -218,6 +215,19 @@ a.sourceLine:hover { visibility: visible; } +/* headroom.js ------------------------ */ + +.headroom { + will-change: transform; + transition: transform 200ms linear; +} +.headroom--pinned { + transform: translateY(0%); +} +.headroom--unpinned { + transform: translateY(-100%); +} + /* mark.js ----------------------------*/ mark { @@ -230,3 +240,17 @@ mark { .html-widget { margin-bottom: 10px; } + +/* fontawesome ------------------------ */ + +.fab { + font-family: "Font Awesome 5 Brands" !important; +} + +/* don't display links in code chunks when printing */ +/* source: https://stackoverflow.com/a/10781533 */ +@media print { + code a:link:after, code a:visited:after { + content: ""; + } +} diff --git a/docs/pkgdown.js b/docs/pkgdown.js index de9bd72..087a762 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -2,14 +2,12 @@ (function($) { $(function() { - $("#sidebar") - .stick_in_parent({offset_top: 40}) - .on('sticky_kit:bottom', function(e) { - $(this).parent().css('position', 'static'); - }) - .on('sticky_kit:unbottom', function(e) { - $(this).parent().css('position', 'relative'); - }); + $('.navbar-fixed-top').headroom(); + + $('body').css('padding-top', $('.navbar').height() + 10); + $(window).resize(function(){ + $('body').css('padding-top', $('.navbar').height() + 10); + }); $('body').scrollspy({ target: '#sidebar', @@ -25,9 +23,13 @@ for (var i = 0; i < links.length; i++) { if (links[i].getAttribute("href") === "#") continue; - var path = paths(links[i].pathname); + // Ignore external links + if (links[i].host !== location.host) + continue; + + var nav_path = paths(links[i].pathname); - var length = prefix_length(cur_path, path); + var length = prefix_length(nav_path, cur_path); if (length > max_length) { max_length = length; pos = i; @@ -52,13 +54,14 @@ return(pieces); } + // Returns -1 if not found function prefix_length(needle, haystack) { if (needle.length > haystack.length) - return(0); + return(-1); // Special case for length-0 haystack, since for loop won't run if (haystack.length === 0) { - return(needle.length === 0 ? 1 : 0); + return(needle.length === 0 ? 0 : -1); } for (var i = 0; i < haystack.length; i++) { @@ -78,9 +81,9 @@ element.setAttribute('data-original-title', tooltipOriginalTitle); } - if(Clipboard.isSupported()) { + if(ClipboardJS.isSupported()) { $(document).ready(function() { - var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>"; + var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-label='Copy to clipboard' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy'></i></button>"; $(".examples, div.sourceCode").addClass("hasCopyButton"); @@ -91,7 +94,7 @@ $('.btn-copy-ex').tooltip({container: 'body'}); // Initialize clipboard: - var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', { + var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', { text: function(trigger) { return trigger.parentNode.textContent; } diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 7908647..8be1490 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,5 @@ pandoc: 2.2.1 -pkgdown: 1.1.0 +pkgdown: 1.4.1 pkgdown_sha: ~ articles: [] diff --git a/docs/reference/IM1xIPC81.html b/docs/reference/IM1xIPC81.html index 3ac5ef7..bd9211c 100644 --- a/docs/reference/IM1xIPC81.html +++ b/docs/reference/IM1xIPC81.html @@ -1,6 +1,6 @@ <!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html> +<html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> @@ -8,21 +8,25 @@ <title>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells — IM1xIPC81 • drfit</title> + <!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" 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> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + +<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" 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"> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <!-- 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> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" 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> +<!-- headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> @@ -30,8 +34,8 @@ -<meta property="og:title" content="Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells — IM1xIPC81" /> +<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 chain length in 3 position on the toxicity to the promyelocytic leukemia rat cell line IPC-81. The substances @@ -46,8 +50,10 @@ + <!-- mathjax --> -<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> <!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> @@ -55,6 +61,7 @@ <![endif]--> + </head> <body> @@ -63,14 +70,15 @@ <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <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">0.7.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.3</span> </span> </div> @@ -78,7 +86,7 @@ <ul class="nav navbar-nav"> <li> <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> + <span class="fas fa fas fa-home fa-lg"></span> </a> </li> @@ -86,7 +94,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -96,6 +103,7 @@ </div><!--/.navbar --> + </header> <div class="row"> @@ -107,7 +115,6 @@ </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 promyelocytic leukemia rat cell line IPC-81. The substances @@ -118,17 +125,16 @@ BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate. 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> - + <pre class="usage"><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>IM1xIPC81</span>)</pre> + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A dataframe containing the data as required for the <code><a href='drfit.html'>drfit</a></code> function. An additional column contains the tested organism (name of the cell line).</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J, @@ -137,7 +143,6 @@ chain lenghts in acute Vibrio fischeri and WST-1 cell viability assays. Ecotoxicology and Environmental Safety 58(3) 396-404</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='no'>rIM1xIPC81</span> <span class='kw'><-</span> <span class='fu'><a href='drfit.html'>drfit</a></span>(<span class='no'>IM1xIPC81</span>, <span class='kw'>linlogit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fl'>10</span>)</div><div class='output co'>#> <span class='message'></span> @@ -158,7 +163,7 @@ #> <span class='message'>IM18 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> #> <span class='message'>IM19 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> #> <span class='message'>IM1-10 BF4: Fitting data...</span></div><div class='input'> - <span class='fu'>print</span>(<span class='no'>rIM1xIPC81</span>,<span class='kw'>digits</span><span class='kw'>=</span><span class='fl'>4</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma + <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>rIM1xIPC81</span>,<span class='kw'>digits</span><span class='kw'>=</span><span class='fl'>4</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma #> 1 IM13 BF4 9 81 0.5918 3.000 inactive NA NA NA microM NA #> 2 IM14 BF4 20 216 -0.0103 3.176 no fit NA NA NA microM NA #> 3 IM15 BF4 9 135 0.5918 3.000 inactive NA NA NA microM NA @@ -175,7 +180,7 @@ #> 5 2.5786 2.300 0.01468 378.941 320.424 458.918 230.782 #> 6 1.6806 2.237 0.05719 47.930 41.973 55.194 27.367 #> 7 1.6496 1.977 0.10956 44.628 39.671 50.483 23.031 -#> 8 0.7697 1.936 0.45809 5.884 4.864 7.152 2.835</div><div class='input'> <span class='fu'>print</span>(<span class='no'>rIM1xIPC81.drc</span>,<span class='kw'>digits</span><span class='kw'>=</span><span class='fl'>4</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma +#> 8 0.7697 1.936 0.45809 5.884 4.864 7.152 2.835</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>rIM1xIPC81.drc</span>,<span class='kw'>digits</span><span class='kw'>=</span><span class='fl'>4</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma #> 1 IM13 BF4 9 81 0.5918 3.000 inactive NA NA NA microM NA #> 2 IM14 BF4 20 216 -0.0103 3.176 linlogit NA NA NA microM 0.1529 #> 3 IM15 BF4 9 135 0.5918 3.000 inactive NA NA NA microM NA @@ -206,24 +211,22 @@ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#format">Format</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> </div> </div> + <footer> <div class="copyright"> <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> </div> </footer> @@ -231,6 +234,8 @@ + </body> </html> + diff --git a/docs/reference/IM1xVibrio.html b/docs/reference/IM1xVibrio.html index 0dde6b0..70381ec 100644 --- a/docs/reference/IM1xVibrio.html +++ b/docs/reference/IM1xVibrio.html @@ -1,6 +1,6 @@ <!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html> +<html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> @@ -8,21 +8,25 @@ <title>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri — IM1xVibrio • drfit</title> + <!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" 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> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + +<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" 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"> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <!-- 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> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" 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> +<!-- headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> @@ -30,8 +34,8 @@ -<meta property="og:title" content="Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri — IM1xVibrio" /> +<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 position on the toxicity to the marine luminescent bacteria V. fischeri. The substances are named according to the UFT naming scheme of @@ -43,8 +47,10 @@ + <!-- mathjax --> -<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> <!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> @@ -52,6 +58,7 @@ <![endif]--> + </head> <body> @@ -60,14 +67,15 @@ <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <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">0.7.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.3</span> </span> </div> @@ -75,7 +83,7 @@ <ul class="nav navbar-nav"> <li> <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> + <span class="fas fa fas fa-home fa-lg"></span> </a> </li> @@ -83,7 +91,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -93,6 +100,7 @@ </div><!--/.navbar --> + </header> <div class="row"> @@ -104,7 +112,6 @@ </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. fischeri</em>. The substances are named according to the UFT naming scheme of @@ -112,29 +119,27 @@ IM13 BF4 means 1-methyl-3-propylimidazolium tetrafluoroborate, 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> - + <pre class="usage"><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>IM1xVibrio</span>)</pre> + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A dataframe containing the data as required for the <code><a href='drfit.html'>drfit</a></code> function. Additional columns contain the species tested (luminescent bacteria Vibrio fischeri, <code>organism</code>), and a field specifying if the data is regarded valid (<code>ok</code>).</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J, Hoffmann J, Ondruschka B, Filser J, Jastorff B (2004) Biological effects of imidazolium ionic liquids with varying chain lenghts in acute Vibrio fischeri and WST-1 cell viability assays. Ecotoxicology and Environmental Safety 58(3) 396-404</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='no'>rIM1xVibrio</span> <span class='kw'><-</span> <span class='fu'><a href='drfit.html'>drfit</a></span>(<span class='no'>IM1xVibrio</span>, <span class='kw'>logit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>chooseone</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>10</span>, <span class='fl'>20</span>))</div><div class='output co'>#> <span class='message'></span> + <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>10</span>, <span class='fl'>20</span>))</div><div class='output co'>#> <span class='message'></span> #> <span class='message'>IM13 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span> #> <span class='message'>IM14 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span> #> <span class='message'>IM15 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span> @@ -142,7 +147,7 @@ #> <span class='message'>IM17 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span> #> <span class='message'>IM18 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span> #> <span class='message'>IM19 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM1-10 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='input'> <span class='fu'>print</span>(<span class='no'>rIM1xVibrio</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>4</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma +#> <span class='message'>IM1-10 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>rIM1xVibrio</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>4</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma #> 1 IM13 BF4 13 22 -5.301 4.699 probit 3.9399 3.8636 4.0160 microM 0.06303 #> 2 IM13 BF4 13 22 -5.301 4.699 logit 3.9461 3.8708 4.0211 microM 0.06188 #> 3 IM14 BF4 12 57 -4.301 4.699 probit 3.5442 3.5030 3.5855 microM 0.05905 @@ -177,7 +182,7 @@ #> 15 -0.1790 0.8019 0.6622 0.5534 7.876e-01 6.212e-02 0.140 #> 16 -0.1831 0.4816 0.6560 0.5470 7.843e-01 5.738e-02 0.141</div><div class='input'> <span class='no'>rIM1xVibrio.drc</span> <span class='kw'><-</span> <span class='fu'><a href='drcfit.html'>drcfit</a></span>(<span class='no'>IM1xVibrio</span>, <span class='kw'>logit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>chooseone</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>10</span>, <span class='fl'>20</span>))</div><div class='output co'>#> <span class='message'></span> + <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>10</span>, <span class='fl'>20</span>))</div><div class='output co'>#> <span class='message'></span> #> <span class='message'>IM13 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> #> <span class='message'>IM14 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> #> <span class='message'>IM15 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> @@ -185,7 +190,7 @@ #> <span class='message'>IM17 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> #> <span class='message'>IM18 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> #> <span class='message'>IM19 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM1-10 BF4: Fitting data...</span></div><div class='input'> <span class='fu'>print</span>(<span class='no'>rIM1xVibrio.drc</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>4</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma +#> <span class='message'>IM1-10 BF4: Fitting data...</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>rIM1xVibrio.drc</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>4</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma #> 1 IM13 BF4 13 22 -5.301 4.699 probit 3.9399 3.8563 4.0100 microM 0.06303 #> 2 IM13 BF4 13 22 -5.301 4.699 logit 3.9461 3.8637 4.0153 microM 0.06188 #> 3 IM14 BF4 12 57 -4.301 4.699 probit 3.5442 3.5009 3.5836 microM 0.05905 @@ -240,24 +245,22 @@ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#format">Format</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> </div> </div> + <footer> <div class="copyright"> <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> </div> </footer> @@ -265,6 +268,8 @@ + </body> </html> + diff --git a/docs/reference/XY.html b/docs/reference/XY.html index 53770a3..4be91cb 100644 --- a/docs/reference/XY.html +++ b/docs/reference/XY.html @@ -1,6 +1,6 @@ <!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html> +<html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> @@ -8,21 +8,25 @@ <title>Dose-Response data for two substances X and Y — XY • drfit</title> + <!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" 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" 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src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> @@ -30,16 +34,18 @@ -<meta property="og:title" content="Dose-Response data for two substances X and Y — XY" /> +<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> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> <!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> @@ -47,6 +53,7 @@ <![endif]--> + </head> <body> @@ -55,14 +62,15 @@ <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <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">0.7.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.3</span> </span> </div> @@ -70,7 +78,7 @@ <ul class="nav navbar-nav"> <li> <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> + <span class="fas fa fas fa-home fa-lg"></span> </a> </li> @@ -78,7 +86,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -88,6 +95,7 @@ </div><!--/.navbar --> + </header> <div class="row"> @@ -99,44 +107,39 @@ </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> - + <pre class="usage"><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>XY</span>)</pre> + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A dataframe containing dose (concentration) and response data, as well as control values where the dose is zero.</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> </div><span class='co'># NOT RUN {</span> -<span class='fu'>demo</span>(<span class='no'>XY</span>) -<span class='co'># }</span></pre> + <pre class="examples"><div class='input'> <span class='kw'>if</span> (<span class='fl'>FALSE</span>) <span class='fu'><a href='https://rdrr.io/r/utils/demo.html'>demo</a></span>(<span class='no'>XY</span>)</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#format">Format</a></li> - <li><a href="#examples">Examples</a></li> </ul> </div> </div> + <footer> <div class="copyright"> <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> </div> </footer> @@ -144,6 +147,8 @@ + </body> </html> + diff --git a/docs/reference/antifoul.html b/docs/reference/antifoul.html index 7ea336a..b3e5604 100644 --- a/docs/reference/antifoul.html +++ b/docs/reference/antifoul.html @@ -1,6 +1,6 @@ <!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html> +<html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> @@ -8,21 +8,25 @@ <title>Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells — antifoul • drfit</title> + <!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" 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> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + +<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" 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"> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <!-- 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> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" 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> +<!-- headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> @@ -30,8 +34,8 @@ -<meta property="og:title" content="Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells — antifoul" /> +<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 @@ -40,8 +44,10 @@ + <!-- mathjax --> -<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> <!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> @@ -49,6 +55,7 @@ <![endif]--> + </head> <body> @@ -57,14 +64,15 @@ <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <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">0.7.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.3</span> </span> </div> @@ -72,7 +80,7 @@ <ul class="nav navbar-nav"> <li> <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> + <span class="fas fa fas fa-home fa-lg"></span> </a> </li> @@ -80,7 +88,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -90,6 +97,7 @@ </div><!--/.navbar --> + </header> <div class="row"> @@ -101,30 +109,28 @@ </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> - + <pre class="usage"><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>antifoul</span>)</pre> + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A dataframe containing 135 and 81 data points for concentrations and responses for TBT and Zink Pyrithione, respectively. Some additional columns from the database are also present.</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>rantifoul.ED50</span> <span class='kw'><-</span> <span class='fu'><a href='drfit.html'>drfit</a></span>(<span class='no'>antifoul</span>, <span class='kw'>linlogit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>logit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>weibull</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>chooseone</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>10</span>))</div><div class='output co'>#> <span class='message'></span> + <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>10</span>))</div><div class='output co'>#> <span class='message'></span> #> <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='input'><span class='fu'>print</span>(<span class='no'>rantifoul.ED50</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>5</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% +#> <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>rantifoul.ED50</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>5</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% #> 1 TBT 38 135 -2.7093 2.3979 linlogit -0.15809 -0.26021 -0.050475 #> 2 TBT 38 135 -2.7093 2.3979 probit -0.16436 -0.26504 -0.056498 #> 3 TBT 38 135 -2.7093 2.3979 logit -0.16012 -0.26116 -0.052591 @@ -154,9 +160,9 @@ <span class='no'>rantifoul.drc</span> <span class='kw'><-</span> <span class='fu'><a href='drcfit.html'>drcfit</a></span>(<span class='no'>antifoul</span>, <span class='kw'>linlogit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>logit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>weibull</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>chooseone</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>10</span>))</div><div class='output co'>#> <span class='message'></span> + <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>10</span>))</div><div class='output co'>#> <span class='message'></span> #> <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='input'><span class='fu'>print</span>(<span class='no'>rantifoul.drc</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>5</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% +#> <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>rantifoul.drc</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>5</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% #> 1 TBT 38 135 -2.7093 2.3979 linlogit NA NA NA #> 2 TBT 38 135 -2.7093 2.3979 probit -0.16436 -0.28178 -0.072022 #> 3 TBT 38 135 -2.7093 2.3979 logit -0.16012 -0.27782 -0.067603 @@ -187,22 +193,21 @@ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#format">Format</a></li> - <li><a href="#examples">Examples</a></li> </ul> </div> </div> + <footer> <div class="copyright"> <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> </div> </footer> @@ -210,6 +215,8 @@ + </body> </html> + diff --git a/docs/reference/checkcontrols.html b/docs/reference/checkcontrols.html index 30baaed..6fa239b 100644 --- a/docs/reference/checkcontrols.html +++ b/docs/reference/checkcontrols.html @@ -1,6 +1,6 @@ <!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html> +<html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> @@ -8,21 +8,25 @@ <title>Check raw data from range of plates or experiments — checkcontrols • drfit</title> + <!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" 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" 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href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <!-- 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> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" 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> +<!-- headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> @@ -30,16 +34,18 @@ -<meta property="og:title" content="Check raw data from range of plates or experiments — checkcontrols" /> +<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> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> <!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> @@ -47,6 +53,7 @@ <![endif]--> + </head> <body> @@ -55,14 +62,15 @@ <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <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">0.7.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.3</span> </span> </div> @@ -70,7 +78,7 @@ <ul class="nav navbar-nav"> <li> <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> + <span class="fas fa fas fa-home fa-lg"></span> </a> </li> @@ -78,7 +86,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -88,6 +95,7 @@ </div><!--/.navbar --> + </header> <div class="row"> @@ -99,18 +107,16 @@ </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='fu'>c</span>(<span class='st'>"cytotox"</span>, <span class='st'>"enzymes"</span>, <span class='st'>"ecotox"</span>), + <span class='kw'>db</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"cytotox"</span>, <span class='st'>"enzymes"</span>, <span class='st'>"ecotox"</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> - + <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'><a href='https://rdrr.io/r/base/c.html'>c</a></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> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> @@ -156,42 +162,36 @@ xbar chart (showing means) are generated.</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>The function lists a report and shows two graphs.</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><span class='co'># NOT RUN {</span> -<span class='fu'>checkcontrols</span>(<span class='fl'>15</span>) -<span class='co'># }</span></pre> + <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) <span class='fu'>checkcontrols</span>(<span class='fl'>15</span>)</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#examples">Examples</a></li> </ul> <h2>Author</h2> - - Johannes Ranke - <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> - + <p>Johannes Ranke + <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a></p> </div> </div> + <footer> <div class="copyright"> <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> </div> </footer> @@ -199,6 +199,8 @@ + </body> </html> + diff --git a/docs/reference/checkexperiment.html b/docs/reference/checkexperiment.html index 937b8dc..7acd323 100644 --- a/docs/reference/checkexperiment.html +++ b/docs/reference/checkexperiment.html @@ -1,6 +1,6 @@ <!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html> +<html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> @@ -8,21 +8,25 @@ <title>Check raw data from a specified experiment or microtiter plate — checkexperiment • drfit</title> + <!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" 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" 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integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <!-- 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> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" 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> +<!-- headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> @@ -30,16 +34,18 @@ -<meta property="og:title" content="Check raw data from a specified experiment or microtiter plate — checkexperiment" /> +<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> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> <!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> @@ -47,6 +53,7 @@ <![endif]--> + </head> <body> @@ -55,14 +62,15 @@ <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <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">0.7.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.3</span> </span> </div> @@ -70,7 +78,7 @@ <ul class="nav navbar-nav"> <li> <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> + <span class="fas fa fas fa-home fa-lg"></span> </a> </li> @@ -78,7 +86,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -88,6 +95,7 @@ </div><!--/.navbar --> + </header> <div class="row"> @@ -99,15 +107,14 @@ </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='fu'>c</span>(<span class='st'>"cytotox"</span>, <span class='st'>"enzymes"</span>)) - <span class='fu'>checkexperiment</span>(<span class='no'>id</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"ecotox"</span>, <span class='st'>"cytotox"</span>, <span class='st'>"enzymes"</span>), <span class='kw'>endpoint</span> <span class='kw'>=</span> <span class='st'>"%"</span>)</pre> - + <pre class="usage"><span class='fu'>checkplate</span>(<span class='no'>id</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"cytotox"</span>, <span class='st'>"enzymes"</span>)) + <span class='fu'>checkexperiment</span>(<span class='no'>id</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"ecotox"</span>, <span class='st'>"cytotox"</span>, <span class='st'>"enzymes"</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>)</pre> + <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> @@ -126,44 +133,47 @@ <td><p>The endpoint that should be used for selecting the data. Only important if the database "ecotox" is used. Defaults to "%".</p></td> </tr> + <tr> + <th>whereClause</th> + <td><p>With this argument, additional conditions for the SQL query can be set, + e.g. "duration = 48" (i.e. "Only retrieve data with duration 48"). The + default is 1 (in SQL syntax this means TRUE).</p></td> + </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>The function lists a report and shows two graphs.</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'># Check plate number 3 in the cytotox database -</div><span class='co'># NOT RUN {</span> -<span class='fu'>checkplate</span>(<span class='fl'>3</span>) -<span class='co'># }</span></pre> + <pre class="examples"><div class='input'><span class='co'># Check plate number 3 in the cytotox database</span> +<span class='kw'>if</span> (<span class='fl'>FALSE</span>) <span class='fu'>checkplate</span>(<span class='fl'>3</span>) + +<span class='co'># Check data from experiment 1517 with duration 48 hours</span> +<span class='kw'>if</span> (<span class='fl'>FALSE</span>) <span class='fu'>checkexperiment</span>(<span class='fl'>1517</span>, <span class='kw'>whereClause</span> <span class='kw'>=</span> <span class='st'>"duration = 48"</span>)</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#examples">Examples</a></li> </ul> <h2>Author</h2> - - Johannes Ranke - <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> - + <p>Johannes Ranke + <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a></p> </div> </div> + <footer> <div class="copyright"> <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> </div> </footer> @@ -171,6 +181,8 @@ + </body> </html> + diff --git a/docs/reference/checksubstance.html b/docs/reference/checksubstance.html index 9f5899c..39bcd4a 100644 --- a/docs/reference/checksubstance.html +++ b/docs/reference/checksubstance.html @@ -1,6 +1,6 @@ <!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html> +<html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> @@ -8,21 +8,25 @@ <title>Check raw data for a specified substance — checksubstance • drfit</title> + <!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" 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> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + +<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" 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"> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <!-- 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> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" 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> +<!-- headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> @@ -30,16 +34,18 @@ -<meta property="og:title" content="Check raw data for a specified substance — checksubstance" /> +<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> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> <!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> @@ -47,6 +53,7 @@ <![endif]--> + </head> <body> @@ -55,14 +62,15 @@ <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <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">0.7.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.3</span> </span> </div> @@ -70,7 +78,7 @@ <ul class="nav navbar-nav"> <li> <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> + <span class="fas fa fas fa-home fa-lg"></span> </a> </li> @@ -78,7 +86,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -88,6 +95,7 @@ </div><!--/.navbar --> + </header> <div class="row"> @@ -99,19 +107,17 @@ </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='fu'>c</span>(<span class='st'>"cytotox"</span>, <span class='st'>"enzymes"</span>, <span class='st'>"ecotox"</span>), + <span class='kw'>db</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"cytotox"</span>, <span class='st'>"enzymes"</span>, <span class='st'>"ecotox"</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> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> @@ -163,43 +169,37 @@ specified substance.</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>The function lists a report and shows one graph.</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'># Check substance IM14 BF4 in the cytotox database -</div><span class='co'># NOT RUN {</span> -<span class='fu'>checksubstance</span>(<span class='st'>"IM14 BF4"</span>) -<span class='co'># }</span></pre> + <pre class="examples"><div class='input'><span class='co'># Check substance IM14 BF4 in the cytotox database</span> +<span class='kw'>if</span> (<span class='fl'>FALSE</span>) <span class='fu'>checksubstance</span>(<span class='st'>"IM14 BF4"</span>)</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#examples">Examples</a></li> </ul> <h2>Author</h2> - - Johannes Ranke - <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> - + <p>Johannes Ranke + <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a></p> </div> </div> + <footer> <div class="copyright"> <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> </div> </footer> @@ -207,6 +207,8 @@ + </body> </html> + diff --git a/docs/reference/drcfit.html b/docs/reference/drcfit.html index b4c299b..1930a24 100644 --- a/docs/reference/drcfit.html +++ b/docs/reference/drcfit.html @@ -1,6 +1,6 @@ <!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html> +<html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> @@ -8,21 +8,25 @@ <title>Fit dose-response models using the drc package — drcfit • drfit</title> + <!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" 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 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integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <!-- 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> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" 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> +<!-- headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> @@ -30,16 +34,18 @@ -<meta property="og:title" content="Fit dose-response models using the drc package — drcfit" /> +<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> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> <!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> @@ -47,6 +53,7 @@ <![endif]--> + </head> <body> @@ -55,14 +62,15 @@ <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <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">0.7.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.3</span> </span> </div> @@ -70,7 +78,7 @@ <ul class="nav navbar-nav"> <li> <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> + <span class="fas fa fas fa-home fa-lg"></span> </a> </li> @@ -78,7 +86,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -88,6 +95,7 @@ </div><!--/.navbar --> + </header> <div class="row"> @@ -99,16 +107,14 @@ </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> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> @@ -136,7 +142,7 @@ <tr> <th>logit</th> <td><p>A boolean defining if cumulative density curves of logistic distributions - <code>plogis</code> are fitted to the decadic logarithm of the dose. + <code><a href='https://rdrr.io/r/stats/Logistic.html'>plogis</a></code> are fitted to the decadic logarithm of the dose. Default is FALSE. Again the parameter definitions used in the model are different to the ones used in <code><a href='drfit.html'>drfit</a></code>. Parameter e from <code>LL.2</code> is listed @@ -179,11 +185,11 @@ scale (not log scale) is included in the output.</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>A dataframe with the attribute <code>models</code> holding a list of the fitted - dose-response models of class <code>nls</code>. The dataframe has at least + dose-response models of class <code><a href='https://rdrr.io/r/stats/nls.html'>nls</a></code>. The dataframe has at least one line for each substance.</p> <p>The following variables are in the dataframe:</p> <dt>Substance</dt><dd><p>The name of the substance</p></dd> @@ -222,24 +228,21 @@ the corresponding dose levels are given in addition, together with their confidence intervals as calculated by ED from the drc package. - <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> <p>There is a demo for each dataset that can be accessed by - <code>demo(dataset)</code></p> - + <code><a href='https://rdrr.io/r/utils/demo.html'>demo(dataset)</a></code></p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> <div class='dont-index'><p>Further examples are given in help pages to the datasets <code><a href='antifoul.html'>antifoul</a></code>, <code><a href='IM1xIPC81.html'>IM1xIPC81</a></code> and <code><a href='IM1xVibrio.html'>IM1xVibrio</a></code>.</p></div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>antifoul</span>) -<span class='no'>r</span> <span class='kw'><-</span> <span class='fu'>drcfit</span>(<span class='no'>antifoul</span>, <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>5</span>, <span class='fl'>10</span>, <span class='fl'>20</span>))</div><div class='output co'>#> <span class='message'></span> + <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>antifoul</span>) +<span class='no'>r</span> <span class='kw'><-</span> <span class='fu'>drcfit</span>(<span class='no'>antifoul</span>, <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>5</span>, <span class='fl'>10</span>, <span class='fl'>20</span>))</div><div class='output co'>#> <span class='message'></span> #> <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='input'><span class='fu'>format</span>(<span class='no'>r</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma a +#> <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>(<span class='no'>r</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma a #> 1 TBT 38 135 -2.7 2.4 probit -0.16 -0.28 -0.072 microM 0.19 0.68 #> 2 Zn Pyrithion 27 81 -2.1 2.0 probit -0.40 -0.52 -0.303 microM 0.23 0.40 #> b ED50 ED50 2.5% ED50 97.5% EDx5 EDx5 2.5% EDx5 97.5% EDx10 EDx10 2.5% @@ -253,32 +256,27 @@ <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#note">Note</a></li> - <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> </ul> <h2>Author</h2> - - Johannes Ranke <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> + <p>Johannes Ranke <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> The functionality of the drc package used under the hood in this function - was written by Christian Ritz. - + was written by Christian Ritz.</p> </div> </div> + <footer> <div class="copyright"> <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> </div> </footer> @@ -286,6 +284,8 @@ + </body> </html> + diff --git a/docs/reference/drdata.html b/docs/reference/drdata.html index 438f32c..104e190 100644 --- a/docs/reference/drdata.html +++ b/docs/reference/drdata.html @@ -1,6 +1,6 @@ <!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html> +<html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> @@ -8,21 +8,25 @@ <title>Get dose-response data via RODBC — drdata • drfit</title> + <!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" 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rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <!-- 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> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" 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> +<!-- headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> @@ -30,15 +34,17 @@ -<meta property="og:title" content="Get dose-response data via RODBC — drdata" /> +<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> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> <!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> @@ -46,6 +52,7 @@ <![endif]--> + </head> <body> @@ -54,14 +61,15 @@ <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <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">0.7.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.3</span> </span> </div> @@ -69,7 +77,7 @@ <ul class="nav navbar-nav"> <li> <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> + <span class="fas fa fas fa-home fa-lg"></span> </a> </li> @@ -77,7 +85,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -87,6 +94,7 @@ </div><!--/.navbar --> + </header> <div class="row"> @@ -98,16 +106,14 @@ </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> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> @@ -161,7 +167,7 @@ additionally retrieve data which has not yet been checked.</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p></p> @@ -170,7 +176,6 @@ for plate, experimentator, performed (date of test performance), celltype, unit (of the dose/concentration), and for the ok field in the database.</p></dd> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <p>The function is currently only used for retrieving data from the @@ -186,7 +191,6 @@ <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> @@ -197,46 +201,42 @@ <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> - <pre class="examples"><div class='input'> </div><span class='co'># NOT RUN {</span> + <pre class="examples"><div class='input'> <span class='kw'>if</span> (<span class='fl'>FALSE</span>) { + <span class='co'># Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81</span> <span class='co'># cells</span> - <span class='fu'>drdata</span>(<span class='fu'>c</span>(<span class='st'>"TBT"</span>, <span class='st'>"ZnPT2"</span>)) - + <span class='fu'>drdata</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"TBT"</span>, <span class='st'>"ZnPT2"</span>)) -<span class='co'># }</span></pre> + }</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#details">Details</a></li> - <li><a href="#examples">Examples</a></li> </ul> <h2>Author</h2> - - Johannes Ranke - <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> - + <p>Johannes Ranke + <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a></p> </div> </div> + <footer> <div class="copyright"> <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> </div> </footer> @@ -244,6 +244,8 @@ + </body> </html> + diff --git a/docs/reference/drfit-package-1.png b/docs/reference/drfit-package-1.png Binary files differindex 62e80fb..b721d7b 100644 --- a/docs/reference/drfit-package-1.png +++ 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+<!-- headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> @@ -30,15 +34,17 @@ -<meta property="og:title" content="Dose-response data evaluation — drfit-package" /> +<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> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> <!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> @@ -46,6 +52,7 @@ <![endif]--> + </head> <body> @@ -54,14 +61,15 @@ <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <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">0.7.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.3</span> </span> </div> @@ -69,7 +77,7 @@ <ul class="nav navbar-nav"> <li> <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> + <span class="fas fa fas fa-home fa-lg"></span> </a> </li> @@ -77,7 +85,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -87,6 +94,7 @@ </div><!--/.navbar --> + </header> <div class="row"> @@ -98,35 +106,31 @@ </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> <p>There is an introductory article located in <a href='../doc/drfit-Rnews.pdf'>../doc/drfit-Rnews.pdf</a>, which will be published in the R News special edition on the use of R for chemists.</p> - <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> <p>There is a demo for each dataset that can be accessed by - <code>demo(dataset)</code></p> - + <code><a href='https://rdrr.io/r/utils/demo.html'>demo(dataset)</a></code></p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> <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></div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>antifoul</span>) + <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>antifoul</span>) <span class='no'>r</span> <span class='kw'><-</span> <span class='fu'><a href='drfit.html'>drfit</a></span>(<span class='no'>antifoul</span>)</div><div class='output co'>#> <span class='message'></span> #> <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='input'><span class='fu'>format</span>(<span class='no'>r</span>,<span class='kw'>digits</span><span class='kw'>=</span><span class='fl'>2</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma a +#> <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>(<span class='no'>r</span>,<span class='kw'>digits</span><span class='kw'>=</span><span class='fl'>2</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma a #> 1 TBT 38 135 -2.7 2.4 probit -0.16 -0.27 -0.056 microM 0.19 -0.16 #> 2 Zn Pyrithion 27 81 -2.1 2.0 probit -0.40 -0.51 -0.292 microM 0.23 -0.40 #> b @@ -136,30 +140,25 @@ is its user-friendliness.</p></div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#details">Details</a></li> - <li><a href="#note">Note</a></li> - <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> </ul> <h2>Author</h2> - -Author and Maintainer: Johannes Ranke <jranke@uni-bremen.de> - + <p>Author and Maintainer: Johannes Ranke <jranke@uni-bremen.de></p> </div> </div> + <footer> <div class="copyright"> <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> </div> </footer> @@ -167,6 +166,8 @@ Author and Maintainer: Johannes Ranke <jranke@uni-bremen.de> + </body> </html> + diff --git a/docs/reference/drfit.html b/docs/reference/drfit.html index 93c2dae..d707a5f 100644 --- a/docs/reference/drfit.html +++ b/docs/reference/drfit.html @@ -1,6 +1,6 @@ <!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html> +<html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> @@ -8,21 +8,25 @@ <title>Fit dose-response models — drfit • drfit</title> + <!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" 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" 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integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <!-- 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> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" 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> +<!-- headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> @@ -30,16 +34,18 @@ -<meta property="og:title" content="Fit dose-response models — drfit" /> +<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> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> <!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> @@ -47,6 +53,7 @@ <![endif]--> + </head> <body> @@ -55,14 +62,15 @@ <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <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">0.7.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.3</span> </span> </div> @@ -70,7 +78,7 @@ <ul class="nav navbar-nav"> <li> <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> + <span class="fas fa fas fa-home fa-lg"></span> </a> </li> @@ -78,7 +86,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -88,6 +95,7 @@ </div><!--/.navbar --> + </header> <div class="row"> @@ -99,10 +107,8 @@ </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>, @@ -110,7 +116,7 @@ <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>, <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> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> @@ -136,19 +142,19 @@ <tr> <th>probit</th> <td><p>A boolean defining if cumulative density curves of normal distributions - <code>pnorm</code> are fitted against the decadic logarithm of the dose. + <code><a href='https://rdrr.io/r/stats/Normal.html'>pnorm</a></code> are fitted against the decadic logarithm of the dose. Default ist TRUE.</p></td> </tr> <tr> <th>logit</th> <td><p>A boolean defining if cumulative density curves of logistic distributions - <code>plogis</code> are fitted to the decadic logarithm of the dose. + <code><a href='https://rdrr.io/r/stats/Logistic.html'>plogis</a></code> are fitted to the decadic logarithm of the dose. Default is FALSE.</p></td> </tr> <tr> <th>weibull</th> <td><p>A boolean defining if the cumulative density curves of weibull distributions - (<code>pweibull</code> with additionall location parameter and scale=1) + (<code><a href='https://rdrr.io/r/stats/Weibull.html'>pweibull</a></code> with additionall location parameter and scale=1) are fitted to the decadic logarithm of the dose. Default is FALSE. Note that the weibull distribution is fitted here to the log transformed doses which appears to be an uncommon approach.</p></td> @@ -183,17 +189,17 @@ <tr> <th>ps0</th> <td><p>If the probit model is fitted, <code>ps0</code> gives the possibility to adjust - the starting value for the scale parameter of <code>pnorm</code>.</p></td> + the starting value for the scale parameter of <code><a href='https://rdrr.io/r/stats/Normal.html'>pnorm</a></code>.</p></td> </tr> <tr> <th>ls0</th> <td><p>If the logit model is fitted, <code>ls0</code> gives the possibility to adjust - the starting value for the scale parameter of <code>plogis</code>.</p></td> + the starting value for the scale parameter of <code><a href='https://rdrr.io/r/stats/Logistic.html'>plogis</a></code>.</p></td> </tr> <tr> <th>ws0</th> <td><p>If the weibull model is fitted, <code>ws0</code> gives the possibility to adjust - the starting value for the shape parameter of <code>pweibull</code>.</p></td> + the starting value for the shape parameter of <code><a href='https://rdrr.io/r/stats/Weibull.html'>pweibull</a></code>.</p></td> </tr> <tr> <th>b0,f0</th> @@ -215,11 +221,11 @@ <td><p>Tolerance of the effect level, expressed on the response scale from 0 to 1.</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>A dataframe with the attribute <code>models</code> holding a list of the fitted - dose-response models of class <code>nls</code>. The dataframe has at least + dose-response models of class <code><a href='https://rdrr.io/r/stats/nls.html'>nls</a></code>. The dataframe has at least one line for each substance.</p> <p>For the “linlogit”, “logit” and “probit” models, the parameter <code>a</code> that is reported coincides with the logED50, i.e the @@ -244,7 +250,7 @@ The name of the column depends on the requested confidence <code>level</code>.</p></dd> <dt>unit</dt><dd><p>The unit used for the dose levels in the dose-response data</p></dd> <dt>sigma</dt><dd><p>The square root of the estimated variance of the random error as returned - by <code>summary.nls</code>.</p></dd> + by <code><a href='https://rdrr.io/r/stats/summary.nls.html'>summary.nls</a></code>.</p></dd> <dt>a</dt><dd><p>For the “linlogit”, “logit” and “probit” models, the parameter <code>a</code> coincides with the logED50. In the case of the “weibull” model, <code>a</code> is a location parameter.</p></dd> @@ -252,8 +258,8 @@ b from the <code><a href='linlogitf.html'>linlogitf</a></code> function. In the case of “probit” fit it is the standard deviation of the fitted normal distribution, in the case of the “logit” fit it is the <code>scale</code> parameter in the - <code>plogis</code> function, and in the “weibull” fit it is the - <code>shape</code> parameter of the fitted <code>pweibull</code> function.</p></dd> + <code><a href='https://rdrr.io/r/stats/Logistic.html'>plogis</a></code> function, and in the “weibull” fit it is the + <code>shape</code> parameter of the fitted <code><a href='https://rdrr.io/r/stats/Weibull.html'>pweibull</a></code> function.</p></dd> <dt>c</dt><dd><p>Only the “linlogit” fit produces a third parameter <code>c</code> which is the variable f from the <code><a href='linlogitf.html'>linlogitf</a></code> function.</p></dd> If the parameter showED50 was set to TRUE, the ED50 values and their @@ -262,12 +268,10 @@ If one or more response leves were specified in the argument EDx, the corresponding dose levels are given in addition. - <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> <p>There is a demo for each dataset that can be accessed by - <code>demo(dataset)</code></p> - + <code><a href='https://rdrr.io/r/utils/demo.html'>demo(dataset)</a></code></p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> <div class='dont-index'><p>Further examples are given in help pages to the datasets @@ -276,13 +280,12 @@ Since version 0.6.1 of this package, there is a drop-in replacement function <code><a href='drcfit.html'>drcfit</a></code> which internally uses the drc package and also gives confidence intervals for EDx values via this package.</p></div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>antifoul</span>) -<span class='no'>r</span> <span class='kw'><-</span> <span class='fu'>drfit</span>(<span class='no'>antifoul</span>, <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>5</span>, <span class='fl'>10</span>, <span class='fl'>20</span>))</div><div class='output co'>#> <span class='message'></span> + <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>antifoul</span>) +<span class='no'>r</span> <span class='kw'><-</span> <span class='fu'>drfit</span>(<span class='no'>antifoul</span>, <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>5</span>, <span class='fl'>10</span>, <span class='fl'>20</span>))</div><div class='output co'>#> <span class='message'></span> #> <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='input'><span class='fu'>format</span>(<span class='no'>r</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma a +#> <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>(<span class='no'>r</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma a #> 1 TBT 38 135 -2.7 2.4 probit -0.16 -0.27 -0.056 microM 0.19 -0.16 #> 2 Zn Pyrithion 27 81 -2.1 2.0 probit -0.40 -0.51 -0.292 microM 0.23 -0.40 #> b ED50 ED50 2.5% ED50 97.5% EDx5 EDx10 EDx20 @@ -293,31 +296,26 @@ <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#note">Note</a></li> - <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> </ul> <h2>Author</h2> - - Johannes Ranke - <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> - + <p>Johannes Ranke + <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a></p> </div> </div> + <footer> <div class="copyright"> <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> </div> </footer> @@ -325,6 +323,8 @@ + </body> </html> + diff --git a/docs/reference/drplot-1.png b/docs/reference/drplot-1.png Binary files differindex bcddcd1..99ba8f4 100644 --- a/docs/reference/drplot-1.png +++ b/docs/reference/drplot-1.png diff --git a/docs/reference/drplot-2.png b/docs/reference/drplot-2.png Binary files differindex 75a75af..22e0bbf 100644 --- a/docs/reference/drplot-2.png +++ b/docs/reference/drplot-2.png diff --git a/docs/reference/drplot.html b/docs/reference/drplot.html index 24d69a8..ebdcdd7 100644 --- a/docs/reference/drplot.html +++ b/docs/reference/drplot.html @@ -1,6 +1,6 @@ <!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html> +<html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> @@ -8,21 +8,25 @@ <title>Plot dose-response models — drplot • drfit</title> + <!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" 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integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" 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> +<!-- headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> @@ -30,16 +34,18 @@ -<meta property="og:title" content="Plot dose-response models — drplot" /> +<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> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> <!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> @@ -47,6 +53,7 @@ <![endif]--> + </head> <body> @@ -55,14 +62,15 @@ <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <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">0.7.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.3</span> </span> </div> @@ -70,7 +78,7 @@ <ul class="nav navbar-nav"> <li> <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> + <span class="fas fa fas fa-home fa-lg"></span> </a> </li> @@ -78,7 +86,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -88,6 +95,7 @@ </div><!--/.navbar --> + </header> <div class="row"> @@ -99,16 +107,14 @@ </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> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> @@ -179,12 +185,12 @@ <tr> <th>axes</th> <td><p>Specifies if axes should be drawn. Default is TRUE, as in - <code>plot.default</code></p></td> + <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot.default</a></code></p></td> </tr> <tr> <th>frame.plot</th> <td><p>Specifies if the plot should be framed. Default is TRUE, as in - <code>plot.default</code></p></td> + <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot.default</a></code></p></td> </tr> <tr> <th>postscript</th> @@ -240,22 +246,20 @@ be added.</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p></p> <dt>results</dt><dd><p>You will get plots of data and/or the fitted dose-response curves, on the screen and/or as postscript/pdf/png files, depending on the parameters.</p></dd> - <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> <p>There is a demo for each dataset that can be accessed by - <code>demo(dataset)</code></p> - + <code><a href='https://rdrr.io/r/utils/demo.html'>demo(dataset)</a></code></p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>antifoul</span>) + <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>antifoul</span>) <span class='no'>r</span> <span class='kw'><-</span> <span class='fu'><a href='drfit.html'>drfit</a></span>(<span class='no'>antifoul</span>)</div><div class='output co'>#> <span class='message'></span> #> <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span> #> <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='output co'>#> <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> @@ -264,29 +268,25 @@ <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#note">Note</a></li> - <li><a href="#examples">Examples</a></li> </ul> <h2>Author</h2> - - Johannes Ranke - <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> - + <p>Johannes Ranke + <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a></p> </div> </div> + <footer> <div class="copyright"> <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> </div> </footer> @@ -294,6 +294,8 @@ + </body> </html> + diff --git a/docs/reference/index.html b/docs/reference/index.html index b05e223..7203c94 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,6 +1,6 @@ <!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html> +<html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> @@ -8,21 +8,25 @@ <title>Function reference • drfit</title> + <!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" 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> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + +<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" 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"> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <!-- 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> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" 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> +<!-- headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> @@ -30,12 +34,15 @@ + <meta property="og:title" content="Function reference" /> + <!-- mathjax --> -<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> <!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> @@ -43,6 +50,7 @@ <![endif]--> + </head> <body> @@ -51,14 +59,15 @@ <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <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">0.7.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.3</span> </span> </div> @@ -66,7 +75,7 @@ <ul class="nav navbar-nav"> <li> <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> + <span class="fas fa fas fa-home fa-lg"></span> </a> </li> @@ -74,7 +83,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -84,6 +92,7 @@ </div><!--/.navbar --> + </header> <div class="row"> @@ -198,13 +207,14 @@ </div> </div> + <footer> <div class="copyright"> <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> </div> </footer> @@ -212,6 +222,8 @@ + </body> </html> + diff --git a/docs/reference/linlogitf.html b/docs/reference/linlogitf.html index ba854f0..f72ca49 100644 --- a/docs/reference/linlogitf.html +++ b/docs/reference/linlogitf.html @@ -1,6 +1,6 @@ <!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html> +<html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> @@ -8,21 +8,25 @@ <title>Linear-logistic function — linlogitf • drfit</title> + <!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" 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> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + +<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" 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"> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <!-- 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> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" 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> +<!-- headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> @@ -30,16 +34,18 @@ -<meta property="og:title" content="Linear-logistic function — linlogitf" /> +<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> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> <!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> @@ -47,6 +53,7 @@ <![endif]--> + </head> <body> @@ -55,14 +62,15 @@ <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <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">0.7.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.3</span> </span> </div> @@ -70,7 +78,7 @@ <ul class="nav navbar-nav"> <li> <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> + <span class="fas fa fas fa-home fa-lg"></span> </a> </li> @@ -78,7 +86,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -88,6 +95,7 @@ </div><!--/.navbar --> + </header> <div class="row"> @@ -99,14 +107,12 @@ </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> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> @@ -131,43 +137,38 @@ <td><p>One of the parameters describing the curve shape.</p></td> </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>The response at dose x.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> <p>van Ewijk, P. H. and Hoekstra, J. A. (1993) <em>Ecotox Environ Safety</em> <b>25</b> 25-32</p> - </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#references">References</a></li> - </ul> + </ul> <h2>Author</h2> - - Johannes Ranke - <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> - + <p>Johannes Ranke + <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a></p> </div> </div> + <footer> <div class="copyright"> <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> </div> </footer> @@ -175,6 +176,8 @@ + </body> </html> + diff --git a/docs/reference/pyrithione.html b/docs/reference/pyrithione.html index 4e608d3..0175c25 100644 --- a/docs/reference/pyrithione.html +++ b/docs/reference/pyrithione.html @@ -1,6 +1,6 @@ <!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html> +<html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> @@ -8,21 +8,25 @@ <title>Cytotoxicity data for different pyrithionates and related species — pyrithione • drfit</title> + <!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" 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 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src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> @@ -30,8 +34,8 @@ -<meta property="og:title" content="Cytotoxicity data for different pyrithionates and related species — pyrithione" /> +<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." /> @@ -39,8 +43,10 @@ + <!-- mathjax --> -<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> <!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> @@ -48,6 +54,7 @@ <![endif]--> + </head> <body> @@ -56,14 +63,15 @@ <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <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">0.7.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.3</span> </span> </div> @@ -71,7 +79,7 @@ <ul class="nav navbar-nav"> <li> <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> + <span class="fas fa fas fa-home fa-lg"></span> </a> </li> @@ -79,7 +87,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -89,6 +96,7 @@ </div><!--/.navbar --> + </header> <div class="row"> @@ -100,54 +108,47 @@ </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> - + <pre class="usage"><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>pyrithione</span>)</pre> + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A dataframe containing the data as required for the <code><a href='drfit.html'>drfit</a></code> function.</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>Doose C, Ranke J, Stock F, Bottin-Weber U, Jastorff B (2004) Structure-activity relationships of pyrithiones - IPC-81 toxicity tests with antifouling biocide zinc pyrithione and structural analogues. Green Chemistry 6(5) 259-266</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> </div><span class='co'># NOT RUN {</span> -<span class='fu'>demo</span>(<span class='no'>pyrithione</span>) -<span class='co'># }</span></pre> + <pre class="examples"><div class='input'> <span class='kw'>if</span> (<span class='fl'>FALSE</span>) <span class='fu'><a href='https://rdrr.io/r/utils/demo.html'>demo</a></span>(<span class='no'>pyrithione</span>)</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#format">Format</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> </div> </div> + <footer> <div class="copyright"> <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> </div> </footer> @@ -155,6 +156,8 @@ + </body> </html> + |
