From 23528ad9b4f07434b3249f1e48ade1e0d07528bf Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 6 Jun 2018 02:11:57 +0200 Subject: Static documentation rebuilt by pkgdown::build_site() --- DESCRIPTION | 1 + docs/authors.html | 28 +++-- docs/docsearch.css | 148 ++++++++++++++++++++++++ docs/docsearch.js | 85 ++++++++++++++ docs/index.html | 33 ++++-- docs/pkgdown.css | 50 +++++++- docs/pkgdown.js | 160 ++++++++++++++------------ docs/pkgdown.yml | 5 + docs/reference/IM1xIPC81.html | 28 ++++- docs/reference/IM1xVibrio.html | 28 ++++- docs/reference/XY.html | 28 ++++- docs/reference/antifoul.html | 30 ++++- docs/reference/checkcontrols.html | 30 ++++- docs/reference/checkexperiment.html | 30 ++++- docs/reference/checksubstance.html | 30 ++++- docs/reference/drcfit.html | 34 ++++-- docs/reference/drdata.html | 97 +++++++--------- docs/reference/drfit-package-1.png | Bin 60443 -> 64002 bytes docs/reference/drfit-package.html | 34 ++++-- docs/reference/drfit.html | 34 ++++-- docs/reference/drplot-1.png | Bin 0 -> 28404 bytes docs/reference/drplot-2.png | Bin 0 -> 26761 bytes docs/reference/drplot.html | 34 ++++-- docs/reference/index.html | 224 +++++++++++++++++++----------------- docs/reference/linlogitf.html | 30 ++++- docs/reference/pyrithione.html | 28 ++++- man/drplot.Rd | 2 +- 27 files changed, 893 insertions(+), 338 deletions(-) create mode 100644 docs/docsearch.css create mode 100644 docs/docsearch.js create mode 100644 docs/pkgdown.yml create mode 100644 docs/reference/drplot-1.png create mode 100644 docs/reference/drplot-2.png 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 @@ + + + - - - + + + + + + @@ -50,8 +56,12 @@ - drfit + + drfit + 0.7.1 + + @@ -75,15 +86,15 @@ -
-
+
+

Authors

  • -

    Johannes Ranke. Author, maintainer. +

    Johannes Ranke. Author, maintainer.

@@ -105,5 +116,8 @@
+ + + 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,"); + background-repeat: no-repeat; + background-position: 50%; + background-size: 100%; + overflow: hidden; + text-indent: -9000px; + width: 100%; + height: 100%; + display: block; + transform: translate(-8px); +} + +.algolia-autocomplete .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 @@ Dose-Response Data Evaluation • drfit - - + + - drfit + + drfit + 0.7.1 +
+
@@ -102,5 +119,7 @@
+ + 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
  • , and enclosing
  • if in dropdown - var menu_anchor = $(value); + // Add class to parent
  • , and enclosing
  • 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 = ""; + if(Clipboard.isSupported()) { + $(document).ready(function() { + var copyButton = ""; - $(".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 @@ + + + - - - + + + + + + @@ -62,8 +68,12 @@ - drfit + + drfit + 0.7.1 + + @@ -87,12 +98,15 @@ -
    +

    Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells

    + +
    +

    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).

    + 
    data(IM1xIPC81)
    @@ -214,5 +229,8 @@
    + + + 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 @@ + + + - - - + + + + + + @@ -59,8 +65,12 @@ - drfit + + drfit + 0.7.1 +
    +
    @@ -84,12 +95,15 @@ -
    +

    Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri

    + +
    +

    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. @@ -99,6 +113,7 @@ IM14 BF4 means 1-methyl-3-butylimidazolium tetrafluoroborate and IM1-10 BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate.

    + 
    data(IM1xVibrio)
    @@ -248,5 +263,8 @@
    + + + 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 @@ + + + - - - + + + + + + @@ -54,8 +60,12 @@ - drfit + + drfit + 0.7.1 +
    +
    @@ -79,16 +90,20 @@ -
    +

    Dose-Response data for two substances X and Y

    + +
    +

    This is just a sample Lemna growth rate data set for two substances arbitrarily named X and Y.

    + 
    data(XY)
    @@ -133,5 +148,8 @@
    + + + 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 @@ + + + - - - + + + + + + @@ -56,8 +62,12 @@ - drfit + + drfit + 0.7.1 +
    +
    @@ -81,18 +92,22 @@ -
    +

    Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells

    + +
    +

    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

    + 
    data(antifoul)
    @@ -199,5 +214,8 @@
    + + + 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 @@ + + + - - - + + + + + + @@ -54,8 +60,12 @@ - drfit + + drfit + 0.7.1 +
    +
    @@ -79,23 +90,27 @@ -
    +

    Check raw data from range of plates or experiments

    + +
    +

    Report control data from a specified range of microtiter plates or experiments from a specified database.

    + 
    checkcontrols(last = 10, id = NULL, db = "cytotox",
                 celltype = "IPC-81", enzymetype = "AChE",
                 organism = "Vibrio fischeri",
                 endpoint = "%", qcc = c("R", "xbar"))
    -

    Arguments

    +

    Arguments

    @@ -182,5 +197,8 @@ + + + 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 @@ + + + - - - + + + + + + @@ -54,8 +60,12 @@ - drfit + + drfit + 0.7.1 + + @@ -79,21 +90,25 @@ -
    +

    Check raw data from a specified experiment or microtiter plate

    + +
    +

    Report metadata from a specified experiment or microtiter plate from a specified database, box plot controls, and plot the dose-response data.

    + 
    checkplate(id, db = "cytotox")
   checkexperiment(id, db = "ecotox", endpoint = "%")
    -

    Arguments

    +

    Arguments

    @@ -155,5 +170,8 @@ + + + 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 @@ + + + - - - + + + + + + @@ -54,8 +60,12 @@ - drfit + + drfit + 0.7.1 + + @@ -79,23 +90,27 @@ -
    +

    Check raw data for a specified substance

    + +
    +

    Report metadata for a specified substance from a specified database, and plot the data.

    + 
    checksubstance(substance, db = "cytotox", experimentator = "%",
     celltype = "%", enzymetype = "%", organism = "%",
     endpoint = "%",
     whereClause = "1", ok = "%")
    -

    Arguments

    +

    Arguments

    @@ -189,5 +204,8 @@ + + + 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 @@ + + + - - - + + + + + + @@ -54,8 +60,12 @@ - drfit + + drfit + 0.7.1 + + @@ -79,22 +90,26 @@ -
    +

    Fit dose-response models using the drc package

    + +
    +

    Fit dose-response relationships to dose-response data and calculate biometric results for (eco)toxicity evaluation using the drc package

    + 
    drcfit(data, chooseone = TRUE, probit = TRUE, logit = FALSE,
   weibull = FALSE, linlogit = FALSE, level = 0.95,
   showED50 = FALSE, EDx = NULL)
    -

    Arguments

    +

    Arguments

    @@ -215,9 +230,9 @@

    See also

    -

    Further examples are given in help pages to the datasets +

    Further examples are given in help pages to the datasets antifoul, IM1xIPC81 and - IM1xVibrio.

    + IM1xVibrio.

    Examples

    @@ -270,5 +285,8 @@ + + + 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 @@ + + + - - - + + + + + + @@ -53,8 +59,12 @@ - drfit + + drfit + 0.7.1 + + @@ -78,21 +89,25 @@ -
    +

    Get dose-response data via RODBC

    + +
    +

    Get dose-response data from an adequate ODBC data source

    + 
    drdata(substances, experimentator = "%", db = "cytotox", celltype = "IPC-81",
     enzymetype="AChE", organism="Vibrio fischeri", endpoint="Luminescence",
     whereClause = "1", ok = "'ok','no fit'")
    -

    Arguments

    +

    Arguments

    @@ -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 /etc/odbcinst.ini - containing:

    - - - - - - - - - - - -
    - [MySQL]
    - Description = MySQL driver for ODBC
    - Driver = /usr/local/lib/libmyodbc.so
    - Setup = /usr/lib/odbc/libodbcmyS.so

    and the file /etc/odbc.ini containing:

    - - - - - - - - - - - - - - - - - - - - - - - -
    - [cytotox]
    - Description = Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen
    - Driver = MySQL
    - Trace = Yes
    - TraceFile = /tmp/odbc.log
    - Database = cytotox
    - Server = eckehaat
    - Port = 3306
    + containing:

    + + + + + +
    [MySQL]
    Description=MySQL driver for ODBC
    Driver=/usr/local/lib/libmyodbc.so
    Setup=/usr/lib/odbc/libodbcmyS.so
    [MySQL]
    +

    and the file /etc/odbc.ini containing:

    + + + + + + + + + +
    [cytotox]
    Description=Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen
    Driver=MySQL
    Trace=Yes
    TraceFile=/tmp/odbc.log
    Database=cytotox
    Server=eckehaat
    Port=3306
    [cytotox]

    Examples

    @@ -256,5 +240,8 @@
    + + + diff --git a/docs/reference/drfit-package-1.png b/docs/reference/drfit-package-1.png index 64d831f..62e80fb 100644 Binary files a/docs/reference/drfit-package-1.png and b/docs/reference/drfit-package-1.png differ diff --git a/docs/reference/drfit-package.html b/docs/reference/drfit-package.html index 1ce4fed..d2aa326 100644 --- a/docs/reference/drfit-package.html +++ b/docs/reference/drfit-package.html @@ -21,16 +21,22 @@ + + + - - - + + + + + + @@ -53,8 +59,12 @@ - drfit + + drfit + 0.7.1 +
    +
    @@ -78,15 +89,19 @@ -
    +

    Dose-response data evaluation

    + +
    +

    See ../DESCRIPTION

    +

    Details

    @@ -102,9 +117,9 @@ of R for chemists.

    See also

    -

    On CRAN, there is another, more statistically sophisticated package with +

    On CRAN, there is another, more statistically sophisticated package with similar functionality called drc. I think the advantage of my package -is its user-friendliness.

    +is its user-friendliness.

    Examples

    @@ -116,7 +131,7 @@ is its user-friendliness.

    #> 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
    drplot(r,antifoul,overlay=TRUE,bw=FALSE)
    +#> 2 0.42
    drplot(r,antifoul,overlay=TRUE,bw=FALSE)
    + + + 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 @@ + + + - - - + + + + + + @@ -54,8 +60,12 @@ - drfit + + drfit + 0.7.1 + + @@ -79,16 +90,20 @@ -
    +

    Fit dose-response models

    + +
    +

    Fit dose-response relationships to dose-response data and calculate biometric results for (eco)toxicity evaluation

    + 
    drfit(data, startlogED50 = NA, chooseone = TRUE, probit = TRUE, logit = FALSE,
   weibull = FALSE, linlogit = FALSE, level = 0.95, linlogitWrong = NA,
@@ -96,7 +111,7 @@
   showED50 = FALSE,
   EDx = NULL, EDx.tolerance = 1e-4)
    -

    Arguments

    +

    Arguments

    @@ -255,12 +270,12 @@

    See also

    -

    Further examples are given in help pages to the datasets +

    Further examples are given in help pages to the datasets antifoul, IM1xIPC81 and IM1xVibrio. Since version 0.6.1 of this package, there is a drop-in replacement function drcfit which internally uses the drc package and also gives - confidence intervals for EDx values via this package.

    + confidence intervals for EDx values via this package.

    Examples

    @@ -309,5 +324,8 @@ + + + diff --git a/docs/reference/drplot-1.png b/docs/reference/drplot-1.png new file mode 100644 index 0000000..bcddcd1 Binary files /dev/null and b/docs/reference/drplot-1.png differ diff --git a/docs/reference/drplot-2.png b/docs/reference/drplot-2.png new file mode 100644 index 0000000..75a75af Binary files /dev/null and b/docs/reference/drplot-2.png differ diff --git a/docs/reference/drplot.html b/docs/reference/drplot.html index b64d4e5..e5cbb22 100644 --- a/docs/reference/drplot.html +++ b/docs/reference/drplot.html @@ -21,17 +21,23 @@ + + + - - - + + + + + + @@ -54,8 +60,12 @@ - drfit + + drfit + 0.7.1 + + @@ -79,22 +90,26 @@ -
    +

    Plot dose-response models

    + +
    +

    Produce graphics of dose-response data and dose-response relationships either combined or separately, for one or more substances.

    + 
    drplot(drresults, data, dtype, alpha, ctype, path,
      fileprefix, overlay, xlim, ylim, xlab, ylab, axes, frame.plot, postscript,
      pdf, png, bw, pointsize, colors, ltys, pchs, devoff, lpos)
    -

    Arguments

    +

    Arguments

    @@ -243,9 +258,7 @@ 
    data(antifoul)
 r <- drfit(antifoul)
    #> 
 #> TBT: Fitting data...
    #> Waiting for profiling to be done...
    #> 
-#> Zn Pyrithion: Fitting data...
    #> Waiting for profiling to be done...
    # NOT RUN {
-drplot(r,antifoul)
-# }
    +#> Zn Pyrithion: Fitting data...
    #> Waiting for profiling to be done...
    drplot(r,antifoul)
    + + + 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 @@ + + + - - - + + + + + + @@ -50,8 +56,12 @@ - drfit + + drfit + 0.7.1 + + @@ -75,112 +86,108 @@ -
    -
    +
    +
    -

    - Reference - version 0.7.1 -

    +

    Reference

    -
    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -

    All functions

    -

    -
    -

    data

    -

    Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells

    -

    checkcontrols

    -

    Check raw data from range of plates or experiments

    -

    checkplate checkexperiment

    -

    Check raw data from a specified experiment or microtiter plate

    -

    drcfit

    -

    Fit dose-response models using the drc package

    -

    drdata

    -

    Get dose-response data via RODBC

    -

    drfit-package

    -

    Dose-response data evaluation

    -

    drfit

    -

    Fit dose-response models

    -

    drplot

    -

    Plot dose-response models

    -

    data

    -

    Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells

    -

    data

    -

    Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri

    -

    linlogitf

    -

    Linear-logistic function

    -

    data

    -

    Cytotoxicity data for different pyrithionates and related species

    -

    data

    -

    Dose-Response data for two substances X and Y

    -
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +

    All functions

    +

    +
    +

    IM1xIPC81

    +

    Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells

    +

    IM1xVibrio

    +

    Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri

    +

    XY

    +

    Dose-Response data for two substances X and Y

    +

    antifoul

    +

    Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells

    +

    checkcontrols()

    +

    Check raw data from range of plates or experiments

    +

    checkplate() checkexperiment()

    +

    Check raw data from a specified experiment or microtiter plate

    +

    drcfit()

    +

    Fit dose-response models using the drc package

    +

    drdata()

    +

    Get dose-response data via RODBC

    +

    drfit-package

    +

    Dose-response data evaluation

    +

    drfit()

    +

    Fit dose-response models

    +

    drplot()

    +

    Plot dose-response models

    +

    linlogitf()

    +

    Linear-logistic function

    +

    pyrithione

    +

    Cytotoxicity data for different pyrithionates and related species

    + + + 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 @@ + + + - - - + + + + + + @@ -54,8 +60,12 @@ - drfit + + drfit + 0.7.1 +
    + @@ -79,20 +90,24 @@ -
    +

    Linear-logistic function

    + +
    +

    Helper function describing a special type of dose-response curves, showing a stimulus at subtoxic doses.

    + 
    linlogitf(x,k,f,mu,b)
    -

    Arguments

    +

    Arguments

    @@ -159,5 +174,8 @@ + + + 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 @@ + + + - - - + + + + + + @@ -55,8 +61,12 @@ - drfit + + drfit + 0.7.1 + + @@ -80,17 +91,21 @@ -
    +

    Cytotoxicity data for different pyrithionates and related species

    + +
    +

    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.

    + 
    data(pyrithione)
    @@ -138,5 +153,8 @@
    + + + 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)}} -- cgit v1.2.1