From 222dc0a1bd460848be61ec28a0a39b30a9fa60db Mon Sep 17 00:00:00 2001 From: Gregory Jefferis Date: Wed, 21 Aug 2024 03:52:40 +0100 Subject: [PATCH] remove static pkgdown site --- docs/authors.html | 132 ----------------- docs/cran-comments-l1.html | 132 ----------------- docs/docsearch.css | 148 ------------------- docs/docsearch.js | 85 ----------- docs/index.html | 173 ---------------------- docs/link.svg | 12 -- docs/news/index.html | 231 ----------------------------- docs/pkgdown.css | 236 ------------------------------ docs/pkgdown.js | 110 -------------- docs/pkgdown.yml | 5 - docs/reference/RANN-package.html | 148 ------------------- docs/reference/index.html | 160 -------------------- docs/reference/nn2.html | 241 ------------------------------- 13 files changed, 1813 deletions(-) delete mode 100644 docs/authors.html delete mode 100644 docs/cran-comments-l1.html delete mode 100644 docs/docsearch.css delete mode 100644 docs/docsearch.js delete mode 100644 docs/index.html delete mode 100644 docs/link.svg delete mode 100644 docs/news/index.html delete mode 100644 docs/pkgdown.css delete mode 100644 docs/pkgdown.js delete mode 100644 docs/pkgdown.yml delete mode 100644 docs/reference/RANN-package.html delete mode 100644 docs/reference/index.html delete mode 100644 docs/reference/nn2.html diff --git a/docs/authors.html b/docs/authors.html deleted file mode 100644 index 0c55a1c..0000000 --- a/docs/authors.html +++ /dev/null @@ -1,132 +0,0 @@ - - - - - - - - -Authors • RANN - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Authors

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    Gregory Jefferis. Maintainer. -

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Developed by Gregory Jefferis.

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Site built with pkgdown 1.2.0.

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NA

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  • New submission, originally submitted as RANN1
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  • Difference to existing package RANN: Metric used for computing distances. RANN uses L2, RANN.L1 uses L1. The underlying ANN library requires changing of preprocessor defines to change the metric; using two similar R packages seems to be the simplest solution to provide ANN implementations with different metrics for the R community.
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  • Checked against R 3.2.0 on Ubuntu, R-devel (r68301) on Debian and R 3.2.0 and R-devel (r68289) on win-builder
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Developed by Gregory Jefferis.

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Site built with pkgdown 1.2.0.

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- - - - - - diff --git a/docs/docsearch.css b/docs/docsearch.css deleted file mode 100644 index e5f1fe1..0000000 --- a/docs/docsearch.css +++ /dev/null @@ -1,148 +0,0 @@ -/* 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 deleted file mode 100644 index b35504c..0000000 --- a/docs/docsearch.js +++ /dev/null @@ -1,85 +0,0 @@ -$(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 deleted file mode 100644 index 64df235..0000000 --- a/docs/index.html +++ /dev/null @@ -1,173 +0,0 @@ - - - - - - - -Fast Nearest Neighbour Search (Wraps ANN Library) Using L2 Metric • RANN - - - - - - - - - -
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-RANN

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Finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount’s ANN library (v1.1.3). There is support for approximate as well as exact searches, fixed radius searches and bd as well as kd trees.

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This package implements nearest neighbors for the Euclidean (L2) metric. For the Manhattan (L1) metric, install the RANN1 package.

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For further details on the underlying ANN library, see http://www.cs.umd.edu/~mount/ANN.

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-Installation

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-Released versions

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The recommendation is to install the released version from CRAN by doing:

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install.packages("RANN")
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-Bleeding Edge

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You can, however, download the tar ball, and run R CMD INSTALL on it, or use the devtools package to install the development version:

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# install.packages("devtools")
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-devtools::install_github("jefferis/RANN")
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Note: Windows users need Rtools and devtools to install this way.

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-Feedback

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Please feel free to:

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Developed by Gregory Jefferis.

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Site built with pkgdown 1.2.0.

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Changelog

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-RANN 2.6.1 Unreleased -

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-RANN 2.6.0 Unreleased -

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  • remove register key word from libANN code (at request of CRAN, #23)
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-RANN 2.5.1 2017-05-21 -

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  • bug fix wrong result dimensions when query is a vector (#17) thanks to github user dayey1
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-RANN 2.5.0 Unreleased -

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  • completely remove defunct nn function
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  • add note in README about new RANN1 package offering Manhattan (L1) metric as an alternative to Euclidean (L2) metric. Note that RANN1 is only available on github at the time of writing).
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-RANN 2.4.1 2014-07-21 -

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  • fix malformed URL field in DESCRIPTION (K. Hornik)
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-RANN 2.4.0 Unreleased -

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  • fix crashing bug when receving N x 0 input matrix (thanks to Rajaraman V for bug report)
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  • doc: correct documentation of return type and other clarifications.
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-RANN 2.3.0 2013-07-24 -

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  • remove nn() function since underlying get_NN() had memory leaks (noticed by Brian Ripley)
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  • make nn2() use input data as query when query not specified)
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  • add Arya and Mount as authors (in accordance with CRAN policies, again BDR)
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  • add Arya, Mount and University of Maryland in Copyright line (in accordance with CRAN policies, again BDR)
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  • add COPYRIGHT file to make it clear exactly which files are from the ANN library and therefore subject to that library’s copyright.
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-RANN 2.2.1 Unreleased -

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  • fix yet more warnings for CRAN due to presence in ANN of exit(), std:cout and std:cerr
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-RANN 2.2.0 Unreleased -

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  • no user-visible changes in theory
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  • switch to roxygen2 for documentation
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  • use this to provide a NAMESPACE as requested for CRAN
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Developed by Gregory Jefferis.

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Site built with pkgdown 1.2.0.

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- - - - - - diff --git a/docs/pkgdown.css b/docs/pkgdown.css deleted file mode 100644 index 2e4f0cf..0000000 --- a/docs/pkgdown.css +++ /dev/null @@ -1,236 +0,0 @@ -/* 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; - height: 100%; - flex-direction: column; - - padding-top: 60px; -} - -body > .container .row { - flex: 1 0 auto; -} - -footer { - margin-top: 45px; - padding: 35px 0 36px; - border-top: 1px solid #e5e5e5; - color: #666; - display: flex; - flex-shrink: 0; -} -footer p { - margin-bottom: 0; -} -footer div { - flex: 1; -} -footer .pkgdown { - text-align: right; -} -footer p { - margin-bottom: 0; -} - -img.icon { - float: right; -} - -img { - max-width: 100%; -} - -/* Fix bug in bootstrap (only seen in firefox) */ -summary { - display: list-item; -} - -/* Typographic tweaking ---------------------------------*/ - -.contents h1.page-header { - margin-top: calc(-60px + 1em); -} - -/* Section anchors ---------------------------------*/ - -a.anchor { - margin-left: -30px; - display:inline-block; - width: 30px; - height: 30px; - visibility: hidden; - - background-image: url(./link.svg); - background-repeat: no-repeat; - background-size: 20px 20px; - background-position: center center; -} - -.hasAnchor:hover a.anchor { - visibility: visible; -} - -@media (max-width: 767px) { - .hasAnchor:hover a.anchor { - visibility: hidden; - } -} - - -/* Fixes for fixed navbar --------------------------*/ - -.contents h1, .contents h2, .contents h3, .contents h4 { - padding-top: 60px; - margin-top: -40px; -} - -/* Static header placement on mobile devices */ -@media (max-width: 767px) { - .navbar-fixed-top { - position: absolute; - } - .navbar { - padding: 0; - } -} - - -/* Sidebar --------------------------*/ - -#sidebar { - margin-top: 30px; -} -#sidebar h2 { - font-size: 1.5em; - margin-top: 1em; -} - -#sidebar h2:first-child { - margin-top: 0; -} - -#sidebar .list-unstyled li { - margin-bottom: 0.5em; -} - -.orcid { - height: 16px; - vertical-align: middle; -} - -/* Reference index & topics ----------------------------------------------- */ - -.ref-index th {font-weight: normal;} - -.ref-index td {vertical-align: top;} -.ref-index .icon {width: 40px;} -.ref-index .alias {width: 40%;} -.ref-index-icons .alias {width: calc(40% - 40px);} -.ref-index .title {width: 60%;} - -.ref-arguments th {text-align: right; padding-right: 10px;} -.ref-arguments th, .ref-arguments td {vertical-align: top;} -.ref-arguments .name {width: 20%;} -.ref-arguments .desc {width: 80%;} - -/* Nice scrolling for wide elements --------------------------------------- */ - -table { - display: block; - overflow: auto; -} - -/* Syntax highlighting ---------------------------------------------------- */ - -pre { - word-wrap: normal; - word-break: normal; - border: 1px solid #eee; -} - -pre, code { - background-color: #f8f8f8; - color: #333; -} - -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 */ -.kw {color: #264D66;} /* keyword */ -.co {color: #888888;} /* comment */ - -.message { color: black; font-weight: bolder;} -.error { color: orange; font-weight: bolder;} -.warning { color: #6A0366; font-weight: bolder;} - -/* Clipboard --------------------------*/ - -.hasCopyButton { - position: relative; -} - -.btn-copy-ex { - position: absolute; - right: 0; - top: 0; - visibility: hidden; -} - -.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 deleted file mode 100644 index 706ad58..0000000 --- a/docs/pkgdown.js +++ /dev/null @@ -1,110 +0,0 @@ -/* 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 - }); - - $('[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 nav_path = paths(links[i].pathname); - - var length = prefix_length(nav_path, cur_path); - if (length > max_length) { - max_length = length; - pos = i; - } - } - - // Add class to parent
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  • 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 / - - 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); - - // 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(i); - } - - return(haystack.length); - } - - /* 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(ClipboardJS.isSupported()) { - $(document).ready(function() { - var copyButton = ""; - - $(".examples, div.sourceCode").addClass("hasCopyButton"); - - // Insert copy buttons: - $(copyButton).prependTo(".hasCopyButton"); - - // Initialize tooltips: - $('.btn-copy-ex').tooltip({container: 'body'}); - - // Initialize clipboard: - var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', { - text: function(trigger) { - return trigger.parentNode.textContent; - } - }); - - clipboardBtnCopies.on('success', function(e) { - changeTooltipMessage(e.trigger, 'Copied!'); - e.clearSelection(); - }); - - clipboardBtnCopies.on('error', function() { - changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy'); - }); - }); - } -})(window.jQuery || window.$) diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml deleted file mode 100644 index f5d49b8..0000000 --- a/docs/pkgdown.yml +++ /dev/null @@ -1,5 +0,0 @@ -pandoc: 1.19.2.1 -pkgdown: 1.2.0 -pkgdown_sha: ~ -articles: [] - diff --git a/docs/reference/RANN-package.html b/docs/reference/RANN-package.html deleted file mode 100644 index 6d0d30e..0000000 --- a/docs/reference/RANN-package.html +++ /dev/null @@ -1,148 +0,0 @@ - - - - - - - - -Wrapper for Arya and Mount's Approximate Nearest Neighbours (ANN) C++ library — RANN-package • RANN - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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    Wrapper for Arya and Mount's Approximate Nearest Neighbours (ANN) C++ library

    - Source: R/RANN-package.R - -
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    Wrapper for Arya and Mount's Approximate Nearest Neighbours (ANN) C++ library

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    See also

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    nn2

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    Developed by Gregory Jefferis.

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    Site built with pkgdown 1.2.0.

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    Reference

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    All functions

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    RANN-package

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    Wrapper for Arya and Mount's Approximate Nearest Neighbours (ANN) C++ library

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    nn2()

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    Nearest Neighbour Search

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    Developed by Gregory Jefferis.

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    Site built with pkgdown 1.2.0.

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    - - - - - - diff --git a/docs/reference/nn2.html b/docs/reference/nn2.html deleted file mode 100644 index 76e499e..0000000 --- a/docs/reference/nn2.html +++ /dev/null @@ -1,241 +0,0 @@ - - - - - - - - -Nearest Neighbour Search — nn2 • RANN - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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    Nearest Neighbour Search

    - Source: R/nn.R - -
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    Uses a kd-tree to find the p number of near neighbours for each point in an -input/output dataset. The advantage of the kd-tree is that it runs in O(M log -M) time.

    - -
    - - 
    nn2(data, query = data, k = min(10, nrow(data)), treetype = c("kd",
-  "bd"), searchtype = c("standard", "priority", "radius"), radius = 0,
-  eps = 0)
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    Arguments

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    data

    An M x d data.frame or matrix, where each of the -M rows is a point or a (column) vector (where d=1).

    query

    A set of N x d points that will be queried against -data. d, the number of columns, must be the same as -data. If missing, defaults to data.

    k

    The maximum number of nearest neighbours to compute. The default -value is set to the smaller of the number of columnns in data

    treetype

    Character vector specifying the standard 'kd' tree or a -'bd' (box-decomposition, AMNSW98) tree which may perform better for -larger point sets

    searchtype

    See details

    radius

    Radius of search for searchtype='radius'

    eps

    Error bound: default of 0.0 implies exact nearest neighbour search

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    Value

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    A list of length 2 with elements:

    -

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    nn.idx

    A N x k integer matrix returning the near - neighbour indices.

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    nn.dists

    A N x k matrix returning the near - neighbour Euclidean distances.

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    Details

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    The RANN package utilizes the Approximate Near Neighbor (ANN) C++ -library, which can give the exact near neighbours or (as the name suggests) -approximate near neighbours to within a specified error bound. For more -information on the ANN library please visit -http://www.cs.umd.edu/~mount/ANN/.

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    Search types: priority visits cells in increasing order of distance -from the query point, and hence, should converge more rapidly on the true -nearest neighbour, but standard is usually faster for exact searches. -radius only searches for neighbours within a specified radius of the -point. If there are no neighbours then nn.idx will contain 0 and nn.dists -will contain 1.340781e+154 for that point.

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    References

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    Bentley J. L. (1975), Multidimensional binary search trees used - for associative search. Communication ACM, 18:309-517.

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    Arya S. and Mount D. M. (1993), Approximate nearest neighbor searching, - Proc. 4th Ann. ACM-SIAM Symposium on Discrete Algorithms (SODA'93), 271-280.

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    Arya S., Mount D. M., Netanyahu N. S., Silverman R. and Wu A. Y (1998), An - optimal algorithm for approximate nearest neighbor searching, Journal of the - ACM, 45, 891-923.

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    Examples

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-x1 <- runif(100, 0, 2*pi)
-x2 <- runif(100, 0,3)
-DATA <- data.frame(x1, x2)
-nearest <- nn2(DATA,DATA)
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