From 16aadfc099f31741a127cf52f18253d44d88a86a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 1 Mar 2018 11:00:17 +0100 Subject: Static documentation rebuilt using current pkgdown --- docs/authors.html | 16 +++++-- docs/index.html | 50 +++++++++++++------- docs/pkgdown.css | 42 ++++++++++++++++- docs/pkgdown.js | 88 +++++++++++++++++++++++++++++++++++- docs/reference/IM1xIPC81.html | 30 ++++++++++-- docs/reference/IM1xVibrio.html | 27 +++++++++-- docs/reference/XY.html | 22 +++++++-- docs/reference/antifoul.html | 28 +++++++++--- docs/reference/checkcontrols.html | 22 +++++++-- docs/reference/checkexperiment.html | 24 ++++++++-- docs/reference/checksubstance.html | 24 ++++++++-- docs/reference/drcfit.html | 32 +++++++++---- docs/reference/drdata.html | 61 +++++++++++++++---------- docs/reference/drfit-package-1.png | Bin 0 -> 60443 bytes docs/reference/drfit-package.html | 23 ++++++++-- docs/reference/drfit.html | 28 +++++++++--- docs/reference/drplot.html | 28 +++++++++--- docs/reference/index.html | 14 +++++- docs/reference/linlogitf.html | 18 +++++++- docs/reference/pyrithione.html | 23 ++++++++-- 20 files changed, 494 insertions(+), 106 deletions(-) create mode 100644 docs/reference/drfit-package-1.png (limited to 'docs') diff --git a/docs/authors.html b/docs/authors.html index f5e3a8f..3734d36 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -18,12 +18,16 @@ + + - + + + @@ -51,6 +55,12 @@
-

Site built with pkgdown.

+

Site built with pkgdown.

diff --git a/docs/index.html b/docs/index.html index c29a291..d13a554 100644 --- a/docs/index.html +++ b/docs/index.html @@ -8,8 +8,22 @@ Dose-Response Data Evaluation • drfit - - + + + + @@ -28,6 +42,12 @@
-

Site built with pkgdown.

+

Site built with pkgdown.

diff --git a/docs/pkgdown.css b/docs/pkgdown.css index 9c437c7..181fe63 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -34,6 +34,10 @@ img.icon { float: right; } +img { + max-width: 100%; +} + /* Section anchors ---------------------------------*/ a.anchor { @@ -96,6 +100,11 @@ a.anchor { margin-bottom: 0.5em; } +.orcid { + height: 16px; + vertical-align: middle; +} + /* Reference index & topics ----------------------------------------------- */ .ref-index th {font-weight: normal;} @@ -133,15 +142,30 @@ pre, code { color: #333; } -pre img { +pre code { + overflow: auto; + word-wrap: normal; + white-space: pre; +} + +pre .img { + margin: 5px 0; +} + +pre .img img { background-color: #fff; display: block; + height: auto; } code a, pre a { color: #375f84; } +a.sourceLine:hover { + text-decoration: none; +} + .fl {color: #1514b5;} .fu {color: #000000;} /* function */ .ch,.st {color: #036a07;} /* string */ @@ -152,3 +176,19 @@ code a, pre a { .error { color: orange; font-weight: bolder;} .warning { color: #6A0366; font-weight: bolder;} +/* Clipboard --------------------------*/ + +.hasCopyButton { + position: relative; +} + +.btn-copy-ex { + position: absolute; + right: 0; + top: 0; + visibility: hidden; +} + +.hasCopyButton:hover button.btn-copy-ex { + visibility: visible; +} diff --git a/docs/pkgdown.js b/docs/pkgdown.js index c8b38c4..64b20df 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -1,8 +1,94 @@ $(function() { - $("#sidebar").stick_in_parent({offset_top: 40}); + + $("#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 }); + 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); + menu_anchor.parent().addClass("active"); + menu_anchor.closest("li.dropdown").addClass("active"); + } + }); }); + +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); +} + +function is_prefix(needle, haystack) { + if (needle.length > haystack.lengh) + return(false); + + for (var i = 0; i < haystack.length; i++) { + if (needle[i] != haystack[i]) + return(false); + } + + return(true); +} + +/* 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); +} + +if(Clipboard.isSupported()) { + $(document).ready(function() { + var copyButton = ""; + + $(".examples").addClass("hasCopyButton"); + + // Insert copy buttons: + $(copyButton).prependTo(".hasCopyButton"); + + // Initialize tooltips: + $('.btn-copy-ex').tooltip({container: 'body'}); + + // 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('error', function() { + changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy'); + }); + }); +} + diff --git a/docs/reference/IM1xIPC81.html b/docs/reference/IM1xIPC81.html index 6fe9bec..2800440 100644 --- a/docs/reference/IM1xIPC81.html +++ b/docs/reference/IM1xIPC81.html @@ -18,12 +18,28 @@ + + + + + + + @@ -51,6 +67,12 @@
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/drcfit.html b/docs/reference/drcfit.html index d433c41..b208f4b 100644 --- a/docs/reference/drcfit.html +++ b/docs/reference/drcfit.html @@ -18,12 +18,20 @@ + + + + + + + @@ -51,6 +59,12 @@
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/drdata.html b/docs/reference/drdata.html index f4716f1..6387e76 100644 --- a/docs/reference/drdata.html +++ b/docs/reference/drdata.html @@ -18,12 +18,19 @@ + + + + + + + @@ -51,6 +58,12 @@ @@ -235,7 +250,7 @@
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/drfit-package-1.png b/docs/reference/drfit-package-1.png new file mode 100644 index 0000000..64d831f Binary files /dev/null and b/docs/reference/drfit-package-1.png differ diff --git a/docs/reference/drfit-package.html b/docs/reference/drfit-package.html index 9cc3de4..1ce4fed 100644 --- a/docs/reference/drfit-package.html +++ b/docs/reference/drfit-package.html @@ -18,12 +18,19 @@ + + + + + + + @@ -51,6 +58,12 @@ -

    See ../DESCRIPTION

    +

    See ../DESCRIPTION

    Details

    -

    There is an introductory article located in ../doc/drfit-Rnews.pdf, +

    There is an introductory article located in ../doc/drfit-Rnews.pdf, which will be published in the R News special edition on the use of R for chemists.

    @@ -96,14 +109,14 @@ is its user-friendliness.

    Examples

    data(antifoul)
-r <- drfit(antifoul)
    #> 
+r <- drfit(antifoul)
    #> 
 #> TBT: Fitting data...
    #> Waiting for profiling to be done...
    #> 
 #> Zn Pyrithion: Fitting data...
    #> Waiting for profiling to be done...
    format(r,digits=2)
    #>      Substance ndl   n  lld lhd  mtype logED50  2.5%  97.5%   unit sigma     a
 #> 1          TBT  38 135 -2.7 2.4 probit   -0.16 -0.27 -0.056 microM  0.19 -0.16
 #> 2 Zn Pyrithion  27  81 -2.1 2.0 probit   -0.40 -0.51 -0.292 microM  0.23 -0.40
 #>      b
 #> 1 0.68
-#> 2 0.42
    drplot(r,antifoul,overlay=TRUE,bw=FALSE)
    +#> 2 0.42
    drplot(r,antifoul,overlay=TRUE,bw=FALSE)
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/drfit.html b/docs/reference/drfit.html index 52ecb2b..4430a5b 100644 --- a/docs/reference/drfit.html +++ b/docs/reference/drfit.html @@ -18,12 +18,20 @@ + + + + + + + @@ -51,6 +59,12 @@ @@ -289,7 +303,7 @@
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/drplot.html b/docs/reference/drplot.html index 4225966..b64d4e5 100644 --- a/docs/reference/drplot.html +++ b/docs/reference/drplot.html @@ -18,12 +18,20 @@ + + + + + + + @@ -51,6 +59,12 @@
    #> Waiting for profiling to be done...
    # NOT RUN { +drplot(r,antifoul) +# } @@ -258,7 +274,7 @@
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/index.html b/docs/reference/index.html index 896e64d..e3ecd24 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -18,12 +18,16 @@ + + - + + + @@ -51,6 +55,12 @@
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/linlogitf.html b/docs/reference/linlogitf.html index b19426f..deed92a 100644 --- a/docs/reference/linlogitf.html +++ b/docs/reference/linlogitf.html @@ -18,12 +18,20 @@ + + + + + + + @@ -51,6 +59,12 @@ @@ -139,7 +153,7 @@
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    diff --git a/docs/reference/pyrithione.html b/docs/reference/pyrithione.html index ee2cc75..d7b6ced 100644 --- a/docs/reference/pyrithione.html +++ b/docs/reference/pyrithione.html @@ -18,12 +18,21 @@ + + + + + + + @@ -51,6 +60,12 @@
    -

    Site built with pkgdown.

    +

    Site built with pkgdown.

    -- cgit v1.2.1