v1.1.6

.devel/sphinx/news.md

@@ -1,8 +1,8 @@
 # Changelog
 
-## 1.1.5.9001 (under development)
+## 1.1.6 (2024-08-22)
 
-* [PYTHON] The packages now works with *numpy* 2.0.
+* [PYTHON] The package now works with *numpy* 2.0.
 
 
 ## 1.1.5 (2023-10-18)
@@ -46,8 +46,8 @@
 *  [R] `mst.default` now throws an error if any element in the input matrix
    is missing/infinite.
 
-*  [Python] Fixed the call to `mlpack.emst` that stopped working
-   with the new version of `mlpack`.
+*  [Python] The call to `mlpack.emst` that stopped working
+   with the new version of `mlpack` has been fixed.
 
 
 ## 1.1.2 (2022-09-17)

.devel/sphinx/rapi/genieclust-package.md

@@ -6,10 +6,28 @@ See [`genie()`](gclust.md) for more details.
 
 ## Author(s)
 
-[Marek Gagolewski](https://www.gagolewski.com/) and other contributors
+**Maintainer**: Marek Gagolewski <[email protected]> ([ORCID](https://orcid.org/0000-0003-0637-6028)) \[copyright holder\]
+
+Other contributors:
+
+-   Maciej Bartoszuk \[contributor\]
+
+-   Anna Cena \[contributor\]
+
+-   Peter M. Larsen \[contributor\]
 
 ## See Also
 
 The official online manual of <span class="pkg">genieclust</span> at <https://genieclust.gagolewski.com/>
 
 Gagolewski M., <span class="pkg">genieclust</span>: Fast and robust hierarchical clustering, *SoftwareX* 15:100722, 2021, [doi:10.1016/j.softx.2021.100722](https://doi.org/10.1016/j.softx.2021.100722).
+
+Useful links:
+
+-   <https://genieclust.gagolewski.com/>
+
+-   <https://clustering-benchmarks.gagolewski.com/>
+
+-   <https://github.com/gagolews/genieclust>
+
+-   Report bugs at <https://github.com/gagolews/genieclust/issues>

.devel/sphinx/rapi/mst.md

@@ -46,7 +46,7 @@ Time complexity is $O(n^2)$ for the method accepting an object of class `dist` a
 
 If `M` \>= 2, then the mutual reachability distance $m(i,j)$ with smoothing factor `M` (see Campello et al. 2013) is used instead of the chosen \"raw\" distance $d(i,j)$. It holds $m(i, j)=\max(d(i,j), c(i), c(j))$, where $c(i)$ is $d(i, k)$ with $k$ being the (`M`-1)-th nearest neighbour of $i$. This makes \"noise\" and \"boundary\" points being \"pulled away\" from each other. Genie++ clustering algorithm (see [`gclust`](gclust.md)) with respect to the mutual reachability distance gains the ability to identify some observations are noise points.
 
-Note that the case `M` = 2 corresponds to the original distance, but we are determining the 1-nearest neighbours separately as well, which is a bit suboptimal; you can file a feature request if this makes your data analysis tasks too slow.
+Note that the case `M` = 2 corresponds to the original distance, but we determine the 1-nearest neighbours separately as well, which is a bit suboptimal; you can file a feature request if this makes your data analysis tasks too slow.
 
 ## Value
 

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: genieclust
 Type: Package
 Title: Fast and Robust Hierarchical Clustering with Noise Points Detection
-Version: 1.1.5-9002
-Date: 2024-07-25
+Version: 1.1.6
+Date: 2024-08-22
 Authors@R: c(
     person("Marek", "Gagolewski",
         role = c("aut", "cre", "cph"),

NEWS

@@ -1,8 +1,8 @@
 # Changelog
 
-## 1.1.5.9001 (under development)
+## 1.1.6 (2024-08-22)
 
-* [PYTHON] The packages now works with *numpy* 2.0.
+* [PYTHON] The package now works with *numpy* 2.0.
 
 
 ## 1.1.5 (2023-10-18)
@@ -46,8 +46,8 @@
 *  [R] `mst.default` now throws an error if any element in the input matrix
    is missing/infinite.
 
-*  [Python] Fixed the call to `mlpack.emst` that stopped working
-   with the new version of `mlpack`.
+*  [Python] The call to `mlpack.emst` that stopped working
+   with the new version of `mlpack` has been fixed.
 
 
 ## 1.1.2 (2022-09-17)

R/genieclust-package.R

@@ -24,16 +24,11 @@
 #' @description
 #' See \code{\link{genie}()} for more details.
 #'
-#'
-#' @name genieclust-package
-#' @rdname genieclust-package
-#' @aliases genieclust
-#' @docType package
-#'
 #' @useDynLib genieclust, .registration=TRUE
 #' @importFrom Rcpp evalCpp
 #' @importFrom stats hclust
 #' @importFrom stats cutree
 #' @importFrom stats dist
 #' @importFrom utils capture.output
-invisible(NULL)
+#' @keywords internal
+"_PACKAGE"

R/mst.R

@@ -44,8 +44,8 @@
 #' Time complexity is \eqn{O(n^2)} for the method accepting an object of
 #' class \code{dist} and \eqn{O(p n^2)} otherwise.
 #'
-#' If \code{M} >= 2, then the mutual reachability distance \eqn{m(i,j)} with smoothing
-#' factor \code{M} (see Campello et al. 2013)
+#' If \code{M} >= 2, then the mutual reachability distance \eqn{m(i,j)}
+#' with smoothing factor \code{M} (see Campello et al. 2013)
 #' is used instead of the chosen "raw" distance \eqn{d(i,j)}.
 #' It holds \eqn{m(i, j)=\max(d(i,j), c(i), c(j))}, where \eqn{c(i)} is
 #' \eqn{d(i, k)} with \eqn{k} being the (\code{M}-1)-th nearest neighbour of \eqn{i}.
@@ -54,8 +54,8 @@
 #' with respect to the mutual reachability distance gains the ability to
 #' identify some observations are noise points.
 #'
-#' Note that the case \code{M} = 2 corresponds to the original distance, but we are
-#' determining the 1-nearest neighbours separately as well, which is a bit
+#' Note that the case \code{M} = 2 corresponds to the original distance, but we
+#' determine the 1-nearest neighbours separately as well, which is a bit
 #' suboptimal; you can file a feature request if this makes your data analysis
 #' tasks too slow.
 #'

docs/_static/documentation_options.js

@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '1.1.5.9002',
+    VERSION: '1.1.6',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

docs/genieclust.html

@@ -222,7 +222,7 @@
 <a class="sidebar-brand" href="index.html">genieclust</a>
 </span>
 <div class="sidebar-brand">
-1.1.5.9002
+1.1.6
 </div>
 <form class="sidebar-search-container" method="get" action="search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -455,7 +455,7 @@ <h1>Python Package <cite>genieclust</cite> Reference<a class="headerlink" href="
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2024-07-25T16:23:35+0200.
+              Last updated on 2024-08-22T09:48:31+0200.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>
@@ -470,7 +470,7 @@ <h1>Python Package <cite>genieclust</cite> Reference<a class="headerlink" href="
 
     </aside>
   </div>
-</div><script src="_static/documentation_options.js?v=88098e3f"></script>
+</div><script src="_static/documentation_options.js?v=937269b5"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
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docs/genieclust_cluster_validity.html

@@ -222,7 +222,7 @@
 <a class="sidebar-brand" href="index.html">genieclust</a>
 </span>
 <div class="sidebar-brand">
-1.1.5.9002
+1.1.6
 </div>
 <form class="sidebar-search-container" method="get" action="search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -1030,7 +1030,7 @@
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2024-07-25T16:23:35+0200.
+              Last updated on 2024-08-22T09:48:31+0200.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>
@@ -1072,7 +1072,7 @@
 
     </aside>
   </div>
-</div><script src="_static/documentation_options.js?v=88098e3f"></script>
+</div><script src="_static/documentation_options.js?v=937269b5"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/furo.js?v=4e2eecee"></script>

docs/genieclust_compare_partitions.html

@@ -222,7 +222,7 @@
 <a class="sidebar-brand" href="index.html">genieclust</a>
 </span>
 <div class="sidebar-brand">
-1.1.5.9002
+1.1.6
 </div>
 <form class="sidebar-search-container" method="get" action="search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -1092,7 +1092,7 @@
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2024-07-25T16:23:35+0200.
+              Last updated on 2024-08-22T09:48:31+0200.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>
@@ -1140,7 +1140,7 @@
 
     </aside>
   </div>
-</div><script src="_static/documentation_options.js?v=88098e3f"></script>
+</div><script src="_static/documentation_options.js?v=937269b5"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/furo.js?v=4e2eecee"></script>

docs/genieclust_genie.html

@@ -222,7 +222,7 @@
 <a class="sidebar-brand" href="index.html">genieclust</a>
 </span>
 <div class="sidebar-brand">
-1.1.5.9002
+1.1.6
 </div>
 <form class="sidebar-search-container" method="get" action="search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -764,7 +764,7 @@ <h1>genieclust.Genie<a class="headerlink" href="#genieclust-genie" title="Link t
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2024-07-25T16:23:35+0200.
+              Last updated on 2024-08-22T09:48:31+0200.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>
@@ -801,7 +801,7 @@ <h1>genieclust.Genie<a class="headerlink" href="#genieclust-genie" title="Link t
 
     </aside>
   </div>
-</div><script src="_static/documentation_options.js?v=88098e3f"></script>
+</div><script src="_static/documentation_options.js?v=937269b5"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/furo.js?v=4e2eecee"></script>

docs/genieclust_gic.html

@@ -222,7 +222,7 @@
 <a class="sidebar-brand" href="index.html">genieclust</a>
 </span>
 <div class="sidebar-brand">
-1.1.5.9002
+1.1.6
 </div>
 <form class="sidebar-search-container" method="get" action="search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -435,7 +435,7 @@ <h1>genieclust.GIc<a class="headerlink" href="#genieclust-gic" title="Link to th
 <p>Gagolewski M., Bartoszuk M., Cena A.,
 Genie: A new, fast, and outlier-resistant hierarchical clustering
 algorithm, <em>Information Sciences</em> 363, 2016, 8-23.
-doi:10.1016/j.ins.2016.05.003.</p>
+doi:10.1016/j.ins.2016.05.003.ing</p>
 </div>
 <div class="citation" id="r32c47d027f4e-4" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id4">4</a><span class="fn-bracket">]</span></span>
@@ -546,7 +546,7 @@ <h1>genieclust.GIc<a class="headerlink" href="#genieclust-gic" title="Link to th
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2024-07-25T16:23:35+0200.
+              Last updated on 2024-08-22T09:48:31+0200.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>
@@ -583,7 +583,7 @@ <h1>genieclust.GIc<a class="headerlink" href="#genieclust-gic" title="Link to th
 
     </aside>
   </div>
-</div><script src="_static/documentation_options.js?v=88098e3f"></script>
+</div><script src="_static/documentation_options.js?v=937269b5"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
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docs/genieclust_inequality.html

@@ -222,7 +222,7 @@
 <a class="sidebar-brand" href="index.html">genieclust</a>
 </span>
 <div class="sidebar-brand">
-1.1.5.9002
+1.1.6
 </div>
 <form class="sidebar-search-container" method="get" action="search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -590,7 +590,7 @@
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2024-07-25T16:23:35+0200.
+              Last updated on 2024-08-22T09:48:31+0200.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>
@@ -626,7 +626,7 @@
 
     </aside>
   </div>
-</div><script src="_static/documentation_options.js?v=88098e3f"></script>
+</div><script src="_static/documentation_options.js?v=937269b5"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/furo.js?v=4e2eecee"></script>

docs/genieclust_internal.html

@@ -222,7 +222,7 @@
 <a class="sidebar-brand" href="index.html">genieclust</a>
 </span>
 <div class="sidebar-brand">
-1.1.5.9002
+1.1.6
 </div>
 <form class="sidebar-search-container" method="get" action="search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -674,7 +674,7 @@
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2024-07-25T16:23:35+0200.
+              Last updated on 2024-08-22T09:48:31+0200.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>
@@ -731,7 +731,7 @@
 
     </aside>
   </div>
-</div><script src="_static/documentation_options.js?v=88098e3f"></script>
+</div><script src="_static/documentation_options.js?v=937269b5"></script>
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     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
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docs/genieclust_plots.html

@@ -222,7 +222,7 @@
 <a class="sidebar-brand" href="index.html">genieclust</a>
 </span>
 <div class="sidebar-brand">
-1.1.5.9002
+1.1.6
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   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -493,7 +493,7 @@
               Some rights reserved. Licensed under <a href='https://creativecommons.org/licenses/by-nc-nd/4.0/'>CC BY-NC-ND 4.0</a>.
               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2024-07-25T16:23:35+0200.
+              Last updated on 2024-08-22T09:48:31+0200.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>
@@ -528,7 +528,7 @@
 
     </aside>
   </div>
-</div><script src="_static/documentation_options.js?v=88098e3f"></script>
+</div><script src="_static/documentation_options.js?v=937269b5"></script>
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     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
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docs/genieclust_tools.html

@@ -222,7 +222,7 @@
 <a class="sidebar-brand" href="index.html">genieclust</a>
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-1.1.5.9002
+1.1.6
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   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -515,7 +515,7 @@
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               Built with <a href="https://sphinx-doc.org/">Sphinx</a>
               and a customised <a href="https://github.com/pradyunsg/furo">Furo</a> theme.
-              Last updated on 2024-07-25T16:23:35+0200.
+              Last updated on 2024-08-22T09:48:31+0200.
               This site will never display any ads: it is a non-profit project.
               It does not collect any data.
             </div>
@@ -551,7 +551,7 @@
 
     </aside>
   </div>
-</div><script src="_static/documentation_options.js?v=88098e3f"></script>
+</div><script src="_static/documentation_options.js?v=937269b5"></script>
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