diff options
27 files changed, 893 insertions, 338 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index 238ed71..4153556 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -24,3 +24,4 @@ LazyLoad: yes LazyData: yes URL: https://pkgdown.jrwb.de/drfit NeedsCompilation: no +RoxygenNote: 6.0.1 diff --git a/docs/authors.html b/docs/authors.html index 3734d36..514359f 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -21,13 +21,19 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="pkgdown.css" rel="stylesheet"> -<script src="jquery.sticky-kit.min.js"></script> <script src="pkgdown.js"></script> - - + + + <meta property="og:title" content="Authors" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -50,8 +56,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="index.html">drfit</a> + <span class="navbar-brand"> + <a class="navbar-link" href="index.html">drfit</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -68,6 +78,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -75,15 +86,15 @@ </header> - <div class="row"> - <div class="contents col-md-12"> +<div class="row"> + <div class="contents col-md-9"> <div class="page-header"> <h1>Authors</h1> </div> <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'></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' height='16'></a> </p> </li> </ul> @@ -105,5 +116,8 @@ </footer> </div> + + </body> </html> + diff --git a/docs/docsearch.css b/docs/docsearch.css new file mode 100644 index 0000000..e5f1fe1 --- /dev/null +++ b/docs/docsearch.css @@ -0,0 +1,148 @@ +/* Docsearch -------------------------------------------------------------- */ +/* + Source: https://github.com/algolia/docsearch/ + License: MIT +*/ + +.algolia-autocomplete { + display: block; + -webkit-box-flex: 1; + -ms-flex: 1; + flex: 1 +} + +.algolia-autocomplete .ds-dropdown-menu { + width: 100%; + min-width: none; + max-width: none; + padding: .75rem 0; + background-color: #fff; + background-clip: padding-box; + border: 1px solid rgba(0, 0, 0, .1); + box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175); +} + +@media (min-width:768px) { + .algolia-autocomplete .ds-dropdown-menu { + width: 175% + } +} + +.algolia-autocomplete .ds-dropdown-menu::before { + display: none +} + +.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] { + padding: 0; + background-color: rgb(255,255,255); + border: 0; + max-height: 80vh; +} + +.algolia-autocomplete .ds-dropdown-menu .ds-suggestions { + margin-top: 0 +} + +.algolia-autocomplete .algolia-docsearch-suggestion { + padding: 0; + overflow: visible +} + +.algolia-autocomplete .algolia-docsearch-suggestion--category-header { + padding: .125rem 1rem; + margin-top: 0; + font-size: 1.3em; + font-weight: 500; + color: #00008B; + border-bottom: 0 +} + +.algolia-autocomplete .algolia-docsearch-suggestion--wrapper { + float: none; + padding-top: 0 +} + +.algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column { + float: none; + width: auto; + padding: 0; + text-align: left +} + +.algolia-autocomplete .algolia-docsearch-suggestion--content { + float: none; + width: auto; + padding: 0 +} + +.algolia-autocomplete .algolia-docsearch-suggestion--content::before { + display: none +} + +.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header { + padding-top: .75rem; + margin-top: .75rem; + border-top: 1px solid rgba(0, 0, 0, .1) +} + +.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column { + display: block; + padding: .1rem 1rem; + margin-bottom: 0.1; + font-size: 1.0em; + font-weight: 400 + /* display: none */ +} + +.algolia-autocomplete .algolia-docsearch-suggestion--title { + display: block; + padding: .25rem 1rem; + margin-bottom: 0; + font-size: 0.9em; + font-weight: 400 +} + +.algolia-autocomplete .algolia-docsearch-suggestion--text { + padding: 0 1rem .5rem; + margin-top: -.25rem; + font-size: 0.8em; + font-weight: 400; + line-height: 1.25 +} + +.algolia-autocomplete .algolia-docsearch-footer { + width: 110px; + height: 20px; + z-index: 3; + margin-top: 10.66667px; + float: right; + font-size: 0; + line-height: 0; +} + +.algolia-autocomplete .algolia-docsearch-footer--logo { + background-image: url("data:image/svg+xml;utf8,<svg viewBox='0 0 130 18' xmlns='http://www.w3.org/2000/svg'><defs><linearGradient x1='-36.868%' y1='134.936%' x2='129.432%' y2='-27.7%' id='a'><stop stop-color='%2300AEFF' offset='0%'/><stop stop-color='%233369E7' offset='100%'/></linearGradient></defs><g fill='none' fill-rule='evenodd'><path d='M59.399.022h13.299a2.372 2.372 0 0 1 2.377 2.364V15.62a2.372 2.372 0 0 1-2.377 2.364H59.399a2.372 2.372 0 0 1-2.377-2.364V2.381A2.368 2.368 0 0 1 59.399.022z' fill='url(%23a)'/><path d='M66.257 4.56c-2.815 0-5.1 2.272-5.1 5.078 0 2.806 2.284 5.072 5.1 5.072 2.815 0 5.1-2.272 5.1-5.078 0-2.806-2.279-5.072-5.1-5.072zm0 8.652c-1.983 0-3.593-1.602-3.593-3.574 0-1.972 1.61-3.574 3.593-3.574 1.983 0 3.593 1.602 3.593 3.574a3.582 3.582 0 0 1-3.593 3.574zm0-6.418v2.664c0 .076.082.131.153.093l2.377-1.226c.055-.027.071-.093.044-.147a2.96 2.96 0 0 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.algolia-docsearch-suggestion--highlight { + color: #FF8C00; + background: rgba(232, 189, 54, 0.1) +} + + +.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight { + box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5) +} + +.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content { + background-color: rgba(192, 192, 192, .15) +} diff --git a/docs/docsearch.js b/docs/docsearch.js new file mode 100644 index 0000000..b35504c --- /dev/null +++ b/docs/docsearch.js @@ -0,0 +1,85 @@ +$(function() { + + // register a handler to move the focus to the search bar + // upon pressing shift + "/" (i.e. "?") + $(document).on('keydown', function(e) { + if (e.shiftKey && e.keyCode == 191) { + e.preventDefault(); + $("#search-input").focus(); + } + }); + + $(document).ready(function() { + // do keyword highlighting + /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */ + var mark = function() { + + var referrer = document.URL ; + var paramKey = "q" ; + + if (referrer.indexOf("?") !== -1) { + var qs = referrer.substr(referrer.indexOf('?') + 1); + var qs_noanchor = qs.split('#')[0]; + var qsa = qs_noanchor.split('&'); + var keyword = ""; + + for (var i = 0; i < qsa.length; i++) { + var currentParam = qsa[i].split('='); + + if (currentParam.length !== 2) { + continue; + } + + if (currentParam[0] == paramKey) { + keyword = decodeURIComponent(currentParam[1].replace(/\+/g, "%20")); + } + } + + if (keyword !== "") { + $(".contents").unmark({ + done: function() { + $(".contents").mark(keyword); + } + }); + } + } + }; + + mark(); + }); +}); + +/* Search term highlighting ------------------------------*/ + +function matchedWords(hit) { + var words = []; + + var hierarchy = hit._highlightResult.hierarchy; + // loop to fetch from lvl0, lvl1, etc. + for (var idx in hierarchy) { + words = words.concat(hierarchy[idx].matchedWords); + } + + var content = hit._highlightResult.content; + if (content) { + words = words.concat(content.matchedWords); + } + + // return unique words + var words_uniq = [...new Set(words)]; + return words_uniq; +} + +function updateHitURL(hit) { + + var words = matchedWords(hit); + var url = ""; + + if (hit.anchor) { + url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor; + } else { + url = hit.url + '?q=' + escape(words.join(" ")); + } + + return url; +} diff --git a/docs/index.html b/docs/index.html index d13a554..98afd7d 100644 --- a/docs/index.html +++ b/docs/index.html @@ -8,8 +8,8 @@ <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><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"> -<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><meta property="og:title" content="Dose-Response Data Evaluation"> +<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"> +<script src="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 @@ -38,8 +38,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="index.html">drfit</a> + <span class="navbar-brand"> + <a class="navbar-link" href="index.html">drfit</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -72,23 +76,36 @@ </div> <div class="col-md-3" id="sidebar"> - <h2>Links</h2> + <div class="links"> +<h2>Links</h2> <ul class="list-unstyled"> -<li>Download from CRAN at <br><a href="https://cran.r-project.org/package=drfit">https://cran.r-project.org/package=drfit</a> +<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"> <h2>License</h2> -<p>GPL (>= 2)</p> +<ul class="list-unstyled"> +<li>GPL (>= 2)</li> +</ul> +</div> +<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"></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" height="16"></a> </li> </ul> +</div> + + <div class="dev-status"> <h2>Dev status</h2> <ul class="list-unstyled"> <li><a href="https://cran.r-project.org/package=drfit"><img src="https://www.r-pkg.org/badges/version/drfit"></a></li> </ul> </div> </div> +</div> <footer><div class="copyright"> @@ -102,5 +119,7 @@ </footer> </div> + + </body> </html> diff --git a/docs/pkgdown.css b/docs/pkgdown.css index 181fe63..6ca2f37 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -1,13 +1,32 @@ -/* Sticker footer */ +/* Sticky footer */ + +/** + * Basic idea: https://philipwalton.github.io/solved-by-flexbox/demos/sticky-footer/ + * Details: https://github.com/philipwalton/solved-by-flexbox/blob/master/assets/css/components/site.css + * + * .Site -> body > .container + * .Site-content -> body > .container .row + * .footer -> footer + * + * Key idea seems to be to ensure that .container and __all its parents__ + * have height set to 100% + * + */ + +html, body { + height: 100%; +} + body > .container { display: flex; - padding-top: 60px; - min-height: calc(100vh); + height: 100%; flex-direction: column; + + padding-top: 60px; } body > .container .row { - flex: 1; + flex: 1 0 auto; } footer { @@ -16,6 +35,7 @@ footer { border-top: 1px solid #e5e5e5; color: #666; display: flex; + flex-shrink: 0; } footer p { margin-bottom: 0; @@ -38,6 +58,12 @@ img { max-width: 100%; } +/* Typographic tweaking ---------------------------------*/ + +.contents h1.page-header { + margin-top: calc(-60px + 1em); +} + /* Section anchors ---------------------------------*/ a.anchor { @@ -68,7 +94,7 @@ a.anchor { .contents h1, .contents h2, .contents h3, .contents h4 { padding-top: 60px; - margin-top: -60px; + margin-top: -40px; } /* Static header placement on mobile devices */ @@ -108,7 +134,6 @@ a.anchor { /* Reference index & topics ----------------------------------------------- */ .ref-index th {font-weight: normal;} -.ref-index h2 {font-size: 20px;} .ref-index td {vertical-align: top;} .ref-index .alias {width: 40%;} @@ -192,3 +217,16 @@ a.sourceLine:hover { .hasCopyButton:hover button.btn-copy-ex { visibility: visible; } + +/* mark.js ----------------------------*/ + +mark { + background-color: rgba(255, 255, 51, 0.5); + border-bottom: 2px solid rgba(255, 153, 51, 0.3); + padding: 1px; +} + +/* vertical spacing after htmlwidgets */ +.html-widget { + margin-bottom: 10px; +} diff --git a/docs/pkgdown.js b/docs/pkgdown.js index 64b20df..de9bd72 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -1,94 +1,110 @@ -$(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) { - $(this).parent().css('position', 'relative'); +/* http://gregfranko.com/blog/jquery-best-practices/ */ +(function($) { + $(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'); + }); + + $('body').scrollspy({ + target: '#sidebar', + offset: 60 }); - $('body').scrollspy({ - target: '#sidebar', - offset: 60 - }); + $('[data-toggle="tooltip"]').tooltip(); + + var cur_path = paths(location.pathname); + var links = $("#navbar ul li a"); + var max_length = -1; + var pos = -1; + for (var i = 0; i < links.length; i++) { + if (links[i].getAttribute("href") === "#") + continue; + var path = paths(links[i].pathname); + + var length = prefix_length(cur_path, path); + if (length > max_length) { + max_length = length; + pos = i; + } + } - var cur_path = paths(location.pathname); - $("#navbar ul li a").each(function(index, value) { - if (value.text == "Home") - return; - if (value.getAttribute("href") === "#") - return; - - var path = paths(value.pathname); - if (is_prefix(cur_path, path)) { - // Add class to parent <li>, and enclosing <li> if in dropdown - var menu_anchor = $(value); + // Add class to parent <li>, and enclosing <li> if in dropdown + if (pos >= 0) { + var menu_anchor = $(links[pos]); menu_anchor.parent().addClass("active"); menu_anchor.closest("li.dropdown").addClass("active"); } }); -}); -function paths(pathname) { - var pieces = pathname.split("/"); - pieces.shift(); // always starts with / + function paths(pathname) { + var pieces = pathname.split("/"); + pieces.shift(); // always starts with / + + var end = pieces[pieces.length - 1]; + if (end === "index.html" || end === "") + pieces.pop(); + return(pieces); + } - var end = pieces[pieces.length - 1]; - if (end === "index.html" || end === "") - pieces.pop(); - return(pieces); -} + function prefix_length(needle, haystack) { + if (needle.length > haystack.length) + return(0); -function is_prefix(needle, haystack) { - if (needle.length > haystack.lengh) - return(false); + // Special case for length-0 haystack, since for loop won't run + if (haystack.length === 0) { + return(needle.length === 0 ? 1 : 0); + } - for (var i = 0; i < haystack.length; i++) { - if (needle[i] != haystack[i]) - return(false); - } + for (var i = 0; i < haystack.length; i++) { + if (needle[i] != haystack[i]) + return(i); + } - return(true); -} + return(haystack.length); + } -/* Clipboard --------------------------*/ + /* Clipboard --------------------------*/ -function changeTooltipMessage(element, msg) { - var tooltipOriginalTitle=element.getAttribute('data-original-title'); - element.setAttribute('data-original-title', msg); - $(element).tooltip('show'); - element.setAttribute('data-original-title', tooltipOriginalTitle); -} + function changeTooltipMessage(element, msg) { + var tooltipOriginalTitle=element.getAttribute('data-original-title'); + element.setAttribute('data-original-title', msg); + $(element).tooltip('show'); + element.setAttribute('data-original-title', tooltipOriginalTitle); + } -if(Clipboard.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>"; + if(Clipboard.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>"; - $(".examples").addClass("hasCopyButton"); + $(".examples, div.sourceCode").addClass("hasCopyButton"); - // Insert copy buttons: - $(copyButton).prependTo(".hasCopyButton"); + // Insert copy buttons: + $(copyButton).prependTo(".hasCopyButton"); - // Initialize tooltips: - $('.btn-copy-ex').tooltip({container: 'body'}); + // Initialize tooltips: + $('.btn-copy-ex').tooltip({container: 'body'}); - // Initialize clipboard: - var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', { - text: function(trigger) { - return trigger.parentNode.textContent; - } - }); + // Initialize clipboard: + var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', { + text: function(trigger) { + return trigger.parentNode.textContent; + } + }); - clipboardBtnCopies.on('success', function(e) { - changeTooltipMessage(e.trigger, 'Copied!'); - e.clearSelection(); - }); + clipboardBtnCopies.on('success', function(e) { + changeTooltipMessage(e.trigger, 'Copied!'); + e.clearSelection(); + }); - clipboardBtnCopies.on('error', function() { - changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy'); + clipboardBtnCopies.on('error', function() { + changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy'); + }); }); - }); -} - + } +})(window.jQuery || window.$) diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml new file mode 100644 index 0000000..6e67788 --- /dev/null +++ b/docs/pkgdown.yml @@ -0,0 +1,5 @@ +pandoc: 1.19.2.4 +pkgdown: 1.1.0 +pkgdown_sha: ~ +articles: [] + diff --git a/docs/reference/IM1xIPC81.html b/docs/reference/IM1xIPC81.html index 2800440..d14afca 100644 --- a/docs/reference/IM1xIPC81.html +++ b/docs/reference/IM1xIPC81.html @@ -21,12 +21,15 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells — IM1xIPC81" /> <meta property="og:description" content="This is the raw data documenting the influence of the alkyl @@ -40,6 +43,9 @@ This is a subset (only the BF4 anion) of the data shown in Figure 3 in Ranke et al. (2004)." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -62,8 +68,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">drfit</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">drfit</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -80,6 +90,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -87,12 +98,15 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells</h1> + + <div class="hidden name"><code>IM1xIPC81.Rd</code></div> </div> + <div class="ref-description"> <p>This is the raw data documenting the influence of the alkyl chain length in 3 position on the toxicity to the @@ -105,6 +119,7 @@ This is a subset (only the BF4 anion) of the data shown in Figure 3 in Ranke et al. (2004).</p> + </div> <pre class="usage"><span class='fu'>data</span>(<span class='no'>IM1xIPC81</span>)</pre> @@ -214,5 +229,8 @@ </footer> </div> + + </body> </html> + diff --git a/docs/reference/IM1xVibrio.html b/docs/reference/IM1xVibrio.html index 22ab40e..594efe1 100644 --- a/docs/reference/IM1xVibrio.html +++ b/docs/reference/IM1xVibrio.html @@ -21,12 +21,15 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri — IM1xVibrio" /> <meta property="og:description" content="This is the raw data documenting the influence of the alkyl chain length in 3 @@ -37,6 +40,9 @@ IM14 BF4 means 1-methyl-3-butylimidazolium tetrafluoroborate and IM1-10 BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -59,8 +65,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">drfit</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">drfit</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -77,6 +87,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -84,12 +95,15 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri</h1> + + <div class="hidden name"><code>IM1xVibrio.Rd</code></div> </div> + <div class="ref-description"> <p>This is the raw data documenting the influence of the alkyl chain length in 3 position on the toxicity to the marine luminescent bacteria <em>V. @@ -99,6 +113,7 @@ IM14 BF4 means 1-methyl-3-butylimidazolium tetrafluoroborate and IM1-10 BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate.</p> + </div> <pre class="usage"><span class='fu'>data</span>(<span class='no'>IM1xVibrio</span>)</pre> @@ -248,5 +263,8 @@ </footer> </div> + + </body> </html> + diff --git a/docs/reference/XY.html b/docs/reference/XY.html index 47ef324..2af3026 100644 --- a/docs/reference/XY.html +++ b/docs/reference/XY.html @@ -21,17 +21,23 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Dose-Response data for two substances X and Y — XY" /> <meta property="og:description" content="This is just a sample Lemna growth rate data set for two substances arbitrarily named X and Y." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">drfit</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">drfit</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -72,6 +82,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -79,16 +90,20 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Dose-Response data for two substances X and Y</h1> + + <div class="hidden name"><code>XY.Rd</code></div> </div> + <div class="ref-description"> <p>This is just a sample Lemna growth rate data set for two substances arbitrarily named X and Y.</p> + </div> <pre class="usage"><span class='fu'>data</span>(<span class='no'>XY</span>)</pre> @@ -133,5 +148,8 @@ </footer> </div> + + </body> </html> + diff --git a/docs/reference/antifoul.html b/docs/reference/antifoul.html index 8dd00c9..d166ebd 100644 --- a/docs/reference/antifoul.html +++ b/docs/reference/antifoul.html @@ -21,19 +21,25 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells — antifoul" /> <meta property="og:description" content="This data set shows the response of the rat leukaemic cell line IPC-81 to dilution series of tributyltin chloride (TBT) and Zink Pyrithione as retrieved - from the "cytotox" database of the UFT Department of Bioorganic Chemistry on + from the "cytotox" database of the UFT Department of Bioorganic Chemistry on February 25, 2004" /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -56,8 +62,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">drfit</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">drfit</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -74,6 +84,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -81,18 +92,22 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells</h1> + + <div class="hidden name"><code>antifoul.Rd</code></div> </div> + <div class="ref-description"> <p>This data set shows the response of the rat leukaemic cell line IPC-81 to dilution series of tributyltin chloride (TBT) and Zink Pyrithione as retrieved from the "cytotox" database of the UFT Department of Bioorganic Chemistry on February 25, 2004</p> + </div> <pre class="usage"><span class='fu'>data</span>(<span class='no'>antifoul</span>)</pre> @@ -199,5 +214,8 @@ </footer> </div> + + </body> </html> + diff --git a/docs/reference/checkcontrols.html b/docs/reference/checkcontrols.html index 2ab3e4d..d3e4314 100644 --- a/docs/reference/checkcontrols.html +++ b/docs/reference/checkcontrols.html @@ -21,17 +21,23 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Check raw data from range of plates or experiments — checkcontrols" /> <meta property="og:description" content="Report control data from a specified range of microtiter plates or experiments from a specified database." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">drfit</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">drfit</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -72,6 +82,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -79,23 +90,27 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Check raw data from range of plates or experiments</h1> + + <div class="hidden name"><code>checkcontrols.Rd</code></div> </div> + <div class="ref-description"> <p>Report control data from a specified range of microtiter plates or experiments from a specified database.</p> + </div> <pre class="usage"><span class='fu'>checkcontrols</span>(<span class='kw'>last</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"cytotox"</span>, <span class='kw'>celltype</span> <span class='kw'>=</span> <span class='st'>"IPC-81"</span>, <span class='kw'>enzymetype</span> <span class='kw'>=</span> <span class='st'>"AChE"</span>, <span class='kw'>organism</span> <span class='kw'>=</span> <span class='st'>"Vibrio fischeri"</span>, <span class='kw'>endpoint</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>qcc</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"R"</span>, <span class='st'>"xbar"</span>))</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -182,5 +197,8 @@ </footer> </div> + + </body> </html> + diff --git a/docs/reference/checkexperiment.html b/docs/reference/checkexperiment.html index 3ec5a09..0712cd4 100644 --- a/docs/reference/checkexperiment.html +++ b/docs/reference/checkexperiment.html @@ -21,17 +21,23 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Check raw data from a specified experiment or microtiter plate — checkexperiment" /> <meta property="og:description" content="Report metadata from a specified experiment or microtiter plate from a specified database, box plot controls, and plot the dose-response data." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">drfit</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">drfit</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -72,6 +82,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -79,21 +90,25 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Check raw data from a specified experiment or microtiter plate</h1> + + <div class="hidden name"><code>checkexperiment.Rd</code></div> </div> + <div class="ref-description"> <p>Report metadata from a specified experiment or microtiter plate from a specified database, box plot controls, and plot the dose-response data.</p> + </div> <pre class="usage"><span class='fu'>checkplate</span>(<span class='no'>id</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"cytotox"</span>) <span class='fu'>checkexperiment</span>(<span class='no'>id</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"ecotox"</span>, <span class='kw'>endpoint</span> <span class='kw'>=</span> <span class='st'>"%"</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -155,5 +170,8 @@ </footer> </div> + + </body> </html> + diff --git a/docs/reference/checksubstance.html b/docs/reference/checksubstance.html index 184a757..3f07df2 100644 --- a/docs/reference/checksubstance.html +++ b/docs/reference/checksubstance.html @@ -21,17 +21,23 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Check raw data for a specified substance — checksubstance" /> <meta property="og:description" content="Report metadata for a specified substance from a specified database, and plot the data." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">drfit</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">drfit</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -72,6 +82,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -79,23 +90,27 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Check raw data for a specified substance</h1> + + <div class="hidden name"><code>checksubstance.Rd</code></div> </div> + <div class="ref-description"> <p>Report metadata for a specified substance from a specified database, and plot the data.</p> + </div> <pre class="usage"><span class='fu'>checksubstance</span>(<span class='no'>substance</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"cytotox"</span>, <span class='kw'>experimentator</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>celltype</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>enzymetype</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>organism</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>endpoint</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>whereClause</span> <span class='kw'>=</span> <span class='st'>"1"</span>, <span class='kw'>ok</span> <span class='kw'>=</span> <span class='st'>"%"</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -189,5 +204,8 @@ </footer> </div> + + </body> </html> + diff --git a/docs/reference/drcfit.html b/docs/reference/drcfit.html index b208f4b..d08b4b0 100644 --- a/docs/reference/drcfit.html +++ b/docs/reference/drcfit.html @@ -21,17 +21,23 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Fit dose-response models using the drc package — drcfit" /> <meta property="og:description" content="Fit dose-response relationships to dose-response data and calculate biometric results for (eco)toxicity evaluation using the drc package" /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">drfit</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">drfit</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -72,6 +82,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -79,22 +90,26 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Fit dose-response models using the drc package</h1> + + <div class="hidden name"><code>drcfit.Rd</code></div> </div> + <div class="ref-description"> <p>Fit dose-response relationships to dose-response data and calculate biometric results for (eco)toxicity evaluation using the drc package</p> + </div> <pre class="usage"><span class='fu'>drcfit</span>(<span class='no'>data</span>, <span class='kw'>chooseone</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>probit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>logit</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>weibull</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>linlogit</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0.95</span>, <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -215,9 +230,9 @@ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p>Further examples are given in help pages to the datasets + <div class='dont-index'><p>Further examples are given in help pages to the datasets <code>antifoul</code>, <code>IM1xIPC81</code> and - <code>IM1xVibrio</code>.</p> + <code>IM1xVibrio</code>.</p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> @@ -270,5 +285,8 @@ </footer> </div> + + </body> </html> + diff --git a/docs/reference/drdata.html b/docs/reference/drdata.html index 6387e76..fc962be 100644 --- a/docs/reference/drdata.html +++ b/docs/reference/drdata.html @@ -21,16 +21,22 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Get dose-response data via RODBC — drdata" /> <meta property="og:description" content="Get dose-response data from an adequate ODBC data source" /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -53,8 +59,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">drfit</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">drfit</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -71,6 +81,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -78,21 +89,25 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Get dose-response data via RODBC</h1> + + <div class="hidden name"><code>drdata.Rd</code></div> </div> + <div class="ref-description"> <p>Get dose-response data from an adequate ODBC data source</p> + </div> <pre class="usage"><span class='fu'>drdata</span>(<span class='no'>substances</span>, <span class='kw'>experimentator</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"cytotox"</span>, <span class='kw'>celltype</span> <span class='kw'>=</span> <span class='st'>"IPC-81"</span>, <span class='kw'>enzymetype</span><span class='kw'>=</span><span class='st'>"AChE"</span>, <span class='kw'>organism</span><span class='kw'>=</span><span class='st'>"Vibrio fischeri"</span>, <span class='kw'>endpoint</span><span class='kw'>=</span><span class='st'>"Luminescence"</span>, <span class='kw'>whereClause</span> <span class='kw'>=</span> <span class='st'>"1"</span>, <span class='kw'>ok</span> <span class='kw'>=</span> <span class='st'>"'ok','no fit'"</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -165,55 +180,24 @@ myODBC. Then, under Unix, you can use iodbc or unixodbc for setting up the respective data source with data source name (DSN) "cytotox". For my setting using unixodbc, I am using the file <code class="file">/etc/odbcinst.ini</code> - containing:</p><table><tr><td> - [MySQL] </td> -<td> </td> -<td> </td> -</tr><tr><td> - Description </td> -<td> = </td> -<td> MySQL driver for ODBC </td> -</tr><tr><td> - Driver </td> -<td> = </td> -<td> /usr/local/lib/libmyodbc.so </td> -</tr><tr><td> - Setup </td> -<td> = </td> -<td> /usr/lib/odbc/libodbcmyS.so </td> -</tr></table><p>and the file <code class="file">/etc/odbc.ini</code> containing:</p><table><tr><td> - [cytotox] </td> -<td> </td> -<td> </td> -</tr><tr><td> - Description </td> -<td> = </td> -<td> Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen </td> -</tr><tr><td> - Driver </td> -<td> = </td> -<td> MySQL </td> -</tr><tr><td> - Trace </td> -<td> = </td> -<td> Yes </td> -</tr><tr><td> - TraceFile </td> -<td> = </td> -<td> /tmp/odbc.log </td> -</tr><tr><td> - Database </td> -<td> = </td> -<td> cytotox </td> -</tr><tr><td> - Server </td> -<td> = </td> -<td> eckehaat </td> -</tr><tr><td> - Port </td> -<td> = </td> -<td> 3306 </td> -</tr></table> + containing:</p><table class='table'> +<tr><td>[MySQL]</td><td></td><td></td></tr> +<tr><td>Description</td><td>=</td><td>MySQL driver for ODBC</td></tr> +<tr><td>Driver</td><td>=</td><td>/usr/local/lib/libmyodbc.so</td></tr> +<tr><td>Setup</td><td>=</td><td>/usr/lib/odbc/libodbcmyS.so</td></tr> +<tr><td></td><td>[MySQL]</td><td></td></tr> +</table> +<p>and the file <code class="file">/etc/odbc.ini</code> containing:</p><table class='table'> +<tr><td>[cytotox]</td><td></td><td></td></tr> +<tr><td>Description</td><td>=</td><td>Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen</td></tr> +<tr><td>Driver</td><td>=</td><td>MySQL</td></tr> +<tr><td>Trace</td><td>=</td><td>Yes</td></tr> +<tr><td>TraceFile</td><td>=</td><td>/tmp/odbc.log</td></tr> +<tr><td>Database</td><td>=</td><td>cytotox</td></tr> +<tr><td>Server</td><td>=</td><td>eckehaat</td></tr> +<tr><td>Port</td><td>=</td><td>3306</td></tr> +<tr><td></td><td>[cytotox]</td><td></td></tr> +</table> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> @@ -256,5 +240,8 @@ </footer> </div> + + </body> </html> + diff --git a/docs/reference/drfit-package-1.png b/docs/reference/drfit-package-1.png Binary files differindex 64d831f..62e80fb 100644 --- a/docs/reference/drfit-package-1.png +++ b/docs/reference/drfit-package-1.png diff --git a/docs/reference/drfit-package.html b/docs/reference/drfit-package.html index 1ce4fed..d2aa326 100644 --- a/docs/reference/drfit-package.html +++ b/docs/reference/drfit-package.html @@ -21,16 +21,22 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Dose-response data evaluation — drfit-package" /> <meta property="og:description" content="See ../DESCRIPTION" /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -53,8 +59,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">drfit</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">drfit</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -71,6 +81,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -78,15 +89,19 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Dose-response data evaluation</h1> + + <div class="hidden name"><code>drfit-package.Rd</code></div> </div> + <div class="ref-description"> <p>See <a href='../DESCRIPTION'>../DESCRIPTION</a></p> + </div> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> @@ -102,9 +117,9 @@ of R for chemists.</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p>On CRAN, there is another, more statistically sophisticated package with + <div class='dont-index'><p>On CRAN, there is another, more statistically sophisticated package with similar functionality called <code>drc</code>. I think the advantage of my package -is its user-friendliness.</p> +is its user-friendliness.</p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> @@ -116,7 +131,7 @@ is its user-friendliness.</p> #> 2 Zn Pyrithion 27 81 -2.1 2.0 probit -0.40 -0.51 -0.292 microM 0.23 -0.40 #> b #> 1 0.68 -#> 2 0.42</div><div class='input'><span class='fu'>drplot</span>(<span class='no'>r</span>,<span class='no'>antifoul</span>,<span class='kw'>overlay</span><span class='kw'>=</span><span class='fl'>TRUE</span>,<span class='kw'>bw</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='img'><img src='drfit-package-1.png' alt='' width='700' height='432.632880098887' /></div></pre> +#> 2 0.42</div><div class='input'><span class='fu'>drplot</span>(<span class='no'>r</span>,<span class='no'>antifoul</span>,<span class='kw'>overlay</span><span class='kw'>=</span><span class='fl'>TRUE</span>,<span class='kw'>bw</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='img'><img src='drfit-package-1.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -150,5 +165,8 @@ Author and Maintainer: Johannes Ranke <jranke@uni-bremen.de> </footer> </div> + + </body> </html> + diff --git a/docs/reference/drfit.html b/docs/reference/drfit.html index 4430a5b..4aa7935 100644 --- a/docs/reference/drfit.html +++ b/docs/reference/drfit.html @@ -21,17 +21,23 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Fit dose-response models — drfit" /> <meta property="og:description" content="Fit dose-response relationships to dose-response data and calculate biometric results for (eco)toxicity evaluation" /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">drfit</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">drfit</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -72,6 +82,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -79,16 +90,20 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Fit dose-response models</h1> + + <div class="hidden name"><code>drfit.Rd</code></div> </div> + <div class="ref-description"> <p>Fit dose-response relationships to dose-response data and calculate biometric results for (eco)toxicity evaluation</p> + </div> <pre class="usage"><span class='fu'>drfit</span>(<span class='no'>data</span>, <span class='kw'>startlogED50</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>chooseone</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>probit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>logit</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>weibull</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>linlogit</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0.95</span>, <span class='kw'>linlogitWrong</span> <span class='kw'>=</span> <span class='fl'>NA</span>, @@ -96,7 +111,7 @@ <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>EDx.tolerance</span> <span class='kw'>=</span> <span class='fl'>1e-4</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -255,12 +270,12 @@ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <p>Further examples are given in help pages to the datasets + <div class='dont-index'><p>Further examples are given in help pages to the datasets <code>antifoul</code>, <code>IM1xIPC81</code> and <code>IM1xVibrio</code>. Since version 0.6.1 of this package, there is a drop-in replacement function <code>drcfit</code> which internally uses the drc package and also gives - confidence intervals for EDx values via this package.</p> + confidence intervals for EDx values via this package.</p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> @@ -309,5 +324,8 @@ </footer> </div> + + </body> </html> + diff --git a/docs/reference/drplot-1.png b/docs/reference/drplot-1.png Binary files differnew file mode 100644 index 0000000..bcddcd1 --- /dev/null +++ b/docs/reference/drplot-1.png diff --git a/docs/reference/drplot-2.png b/docs/reference/drplot-2.png Binary files differnew file mode 100644 index 0000000..75a75af --- /dev/null +++ b/docs/reference/drplot-2.png diff --git a/docs/reference/drplot.html b/docs/reference/drplot.html index b64d4e5..e5cbb22 100644 --- a/docs/reference/drplot.html +++ b/docs/reference/drplot.html @@ -21,17 +21,23 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Plot dose-response models — drplot" /> <meta property="og:description" content="Produce graphics of dose-response data and dose-response relationships either combined or separately, for one or more substances." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">drfit</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">drfit</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -72,6 +82,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -79,22 +90,26 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Plot dose-response models</h1> + + <div class="hidden name"><code>drplot.Rd</code></div> </div> + <div class="ref-description"> <p>Produce graphics of dose-response data and dose-response relationships either combined or separately, for one or more substances.</p> + </div> <pre class="usage"><span class='fu'>drplot</span>(<span class='no'>drresults</span>, <span class='no'>data</span>, <span class='no'>dtype</span>, <span class='no'>alpha</span>, <span class='no'>ctype</span>, <span class='no'>path</span>, <span class='no'>fileprefix</span>, <span class='no'>overlay</span>, <span class='no'>xlim</span>, <span class='no'>ylim</span>, <span class='no'>xlab</span>, <span class='no'>ylab</span>, <span class='no'>axes</span>, <span class='no'>frame.plot</span>, <span class='no'>postscript</span>, <span class='no'>pdf</span>, <span class='no'>png</span>, <span class='no'>bw</span>, <span class='no'>pointsize</span>, <span class='no'>colors</span>, <span class='no'>ltys</span>, <span class='no'>pchs</span>, <span class='no'>devoff</span>, <span class='no'>lpos</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -243,9 +258,7 @@ <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>antifoul</span>) <span class='no'>r</span> <span class='kw'><-</span> <span class='fu'>drfit</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><span class='co'># NOT RUN {</span> -<span class='fu'>drplot</span>(<span class='no'>r</span>,<span class='no'>antifoul</span>) -<span class='co'># }</span></pre> +#> <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> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -280,5 +293,8 @@ </footer> </div> + + </body> </html> + diff --git a/docs/reference/index.html b/docs/reference/index.html index e3ecd24..2b1f884 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -21,13 +21,19 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Function reference" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -50,8 +56,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">drfit</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">drfit</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -68,6 +78,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -75,112 +86,108 @@ </header> - <div class="row"> - <div class="col-md-9"> +<div class="row"> + <div class="contents col-md-9"> <div class="page-header"> - <h1> - Reference - <small>version 0.7.1</small> - </h1> + <h1>Reference</h1> </div> - <div class="contents"> - <table class="ref-index"> - - <colgroup> - <col class="alias" /> - <col class="title" /> - </colgroup> - - <tbody> - <tr> - <th colspan="2"> - <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2> - <p class="section-desc"></p> - </th> - </tr> - <tr> - <!-- --> - <td> - <p><code><a href="antifoul.html">data</a></code> </p> - </td> - <td><p>Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="checkcontrols.html">checkcontrols</a></code> </p> - </td> - <td><p>Check raw data from range of plates or experiments</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="checkexperiment.html">checkplate</a></code> <code><a href="checkexperiment.html">checkexperiment</a></code> </p> - </td> - <td><p>Check raw data from a specified experiment or microtiter plate</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="drcfit.html">drcfit</a></code> </p> - </td> - <td><p>Fit dose-response models using the drc package</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="drdata.html">drdata</a></code> </p> - </td> - <td><p>Get dose-response data via RODBC</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="drfit-package.html">drfit-package</a></code> </p> - </td> - <td><p>Dose-response data evaluation</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="drfit.html">drfit</a></code> </p> - </td> - <td><p>Fit dose-response models</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="drplot.html">drplot</a></code> </p> - </td> - <td><p>Plot dose-response models</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="IM1xIPC81.html">data</a></code> </p> - </td> - <td><p>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="IM1xVibrio.html">data</a></code> </p> - </td> - <td><p>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="linlogitf.html">linlogitf</a></code> </p> - </td> - <td><p>Linear-logistic function</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="pyrithione.html">data</a></code> </p> - </td> - <td><p>Cytotoxicity data for different pyrithionates and related species</p></td> - </tr><tr> - <!-- --> - <td> - <p><code><a href="XY.html">data</a></code> </p> - </td> - <td><p>Dose-Response data for two substances X and Y</p></td> - </tr> - </tbody> - </table> - </div> + <table class="ref-index"> + + <colgroup> + + <col class="alias" /> + <col class="title" /> + </colgroup> + + <tbody> + <tr> + <th colspan="2"> + <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2> + <p class="section-desc"></p> + </th> + </tr> + <tr> + + <td> + <p><code><a href="IM1xIPC81.html">IM1xIPC81</a></code> </p> + </td> + <td><p>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells</p></td> + </tr><tr> + + <td> + <p><code><a href="IM1xVibrio.html">IM1xVibrio</a></code> </p> + </td> + <td><p>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri</p></td> + </tr><tr> + + <td> + <p><code><a href="XY.html">XY</a></code> </p> + </td> + <td><p>Dose-Response data for two substances X and Y</p></td> + </tr><tr> + + <td> + <p><code><a href="antifoul.html">antifoul</a></code> </p> + </td> + <td><p>Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells</p></td> + </tr><tr> + + <td> + <p><code><a href="checkcontrols.html">checkcontrols()</a></code> </p> + </td> + <td><p>Check raw data from range of plates or experiments</p></td> + </tr><tr> + + <td> + <p><code><a href="checkexperiment.html">checkplate()</a></code> <code><a href="checkexperiment.html">checkexperiment()</a></code> </p> + </td> + <td><p>Check raw data from a specified experiment or microtiter plate</p></td> + </tr><tr> + + <td> + <p><code><a href="drcfit.html">drcfit()</a></code> </p> + </td> + <td><p>Fit dose-response models using the drc package</p></td> + </tr><tr> + + <td> + <p><code><a href="drdata.html">drdata()</a></code> </p> + </td> + <td><p>Get dose-response data via RODBC</p></td> + </tr><tr> + + <td> + <p><code><a href="drfit-package.html">drfit-package</a></code> </p> + </td> + <td><p>Dose-response data evaluation</p></td> + </tr><tr> + + <td> + <p><code><a href="drfit.html">drfit()</a></code> </p> + </td> + <td><p>Fit dose-response models</p></td> + </tr><tr> + + <td> + <p><code><a href="drplot.html">drplot()</a></code> </p> + </td> + <td><p>Plot dose-response models</p></td> + </tr><tr> + + <td> + <p><code><a href="linlogitf.html">linlogitf()</a></code> </p> + </td> + <td><p>Linear-logistic function</p></td> + </tr><tr> + + <td> + <p><code><a href="pyrithione.html">pyrithione</a></code> </p> + </td> + <td><p>Cytotoxicity data for different pyrithionates and related species</p></td> + </tr> + </tbody> + </table> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -203,5 +210,8 @@ </footer> </div> + + </body> </html> + diff --git a/docs/reference/linlogitf.html b/docs/reference/linlogitf.html index deed92a..1dddf50 100644 --- a/docs/reference/linlogitf.html +++ b/docs/reference/linlogitf.html @@ -21,17 +21,23 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Linear-logistic function — linlogitf" /> <meta property="og:description" content="Helper function describing a special type of dose-response curves, showing a stimulus at subtoxic doses." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -54,8 +60,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">drfit</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">drfit</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -72,6 +82,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -79,20 +90,24 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Linear-logistic function</h1> + + <div class="hidden name"><code>linlogitf.Rd</code></div> </div> + <div class="ref-description"> <p>Helper function describing a special type of dose-response curves, showing a stimulus at subtoxic doses.</p> + </div> <pre class="usage"><span class='fu'>linlogitf</span>(<span class='no'>x</span>,<span class='no'>k</span>,<span class='no'>f</span>,<span class='no'>mu</span>,<span class='no'>b</span>)</pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> @@ -159,5 +174,8 @@ </footer> </div> + + </body> </html> + diff --git a/docs/reference/pyrithione.html b/docs/reference/pyrithione.html index d7b6ced..1488ecb 100644 --- a/docs/reference/pyrithione.html +++ b/docs/reference/pyrithione.html @@ -21,18 +21,24 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Cytotoxicity data for different pyrithionates and related species — pyrithione" /> <meta property="og:description" content="This data shows the cytotoxicity of pyrithione salts as well as the free pyrithione, its oxidation product and some other related compounds to the IPC-81 cell line." /> <meta name="twitter:card" content="summary" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -55,8 +61,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">drfit</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">drfit</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -73,6 +83,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -80,17 +91,21 @@ </header> - <div class="row"> +<div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Cytotoxicity data for different pyrithionates and related species</h1> + + <div class="hidden name"><code>pyrithione.Rd</code></div> </div> + <div class="ref-description"> <p>This data shows the cytotoxicity of pyrithione salts as well as the free pyrithione, its oxidation product and some other related compounds to the IPC-81 cell line.</p> + </div> <pre class="usage"><span class='fu'>data</span>(<span class='no'>pyrithione</span>)</pre> @@ -138,5 +153,8 @@ </footer> </div> + + </body> </html> + diff --git a/man/drplot.Rd b/man/drplot.Rd index 6b8a7bf..d8d7eb3 100644 --- a/man/drplot.Rd +++ b/man/drplot.Rd @@ -123,7 +123,7 @@ \examples{ data(antifoul) r <- drfit(antifoul) -\dontrun{drplot(r,antifoul)} +drplot(r,antifoul) } \note{There is a demo for each dataset that can be accessed by \code{demo(dataset)}} |
