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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">JDS</journal-id>
<journal-title-group><journal-title>Journal of Data Science</journal-title></journal-title-group>
<issn pub-type="epub">1683-8602</issn><issn pub-type="ppub">1680-743X</issn><issn-l>1680-743X</issn-l>
<publisher>
<publisher-name>School of Statistics, Renmin University of China</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="publisher-id">JDS1110</article-id>
<article-id pub-id-type="doi">10.6339/23-JDS1110</article-id>
<article-categories><subj-group subj-group-type="heading">
<subject>Computing in Data Science</subject></subj-group></article-categories>
<title-group>
<article-title>Generating General Preferential Attachment Networks with <sans-serif>R</sans-serif> Package <italic>wdnet</italic></article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name><surname>Yuan</surname><given-names>Yelie</given-names></name><email xlink:href="mailto:yelie.yuan@uconn.edu">yelie.yuan@uconn.edu</email><xref ref-type="aff" rid="j_jds1110_aff_001">1</xref><xref ref-type="corresp" rid="cor1">∗</xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Wang</surname><given-names>Tiandong</given-names></name><xref ref-type="aff" rid="j_jds1110_aff_002">2</xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Yan</surname><given-names>Jun</given-names></name><xref ref-type="aff" rid="j_jds1110_aff_001">1</xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Zhang</surname><given-names>Panpan</given-names></name><xref ref-type="aff" rid="j_jds1110_aff_003">3</xref>
</contrib>
<aff id="j_jds1110_aff_001"><label>1</label>Department of Statistics, <institution>University of Connecticut</institution>, Storrs, Connecticut, <country>USA</country></aff>
<aff id="j_jds1110_aff_002"><label>2</label>Shanghai Center for Mathematical Sciences, <institution>Fudan University</institution>, Shanghai, <country>China</country></aff>
<aff id="j_jds1110_aff_003"><label>3</label>Department of Biostatistics, <institution>Vanderbilt University Medical Center</institution>, Nashville, Tennessee, <country>USA</country></aff>
</contrib-group>
<author-notes>
<corresp id="cor1"><label>∗</label>Corresponding author. Email: <ext-link ext-link-type="uri" xlink:href="mailto:yelie.yuan@uconn.edu">yelie.yuan@uconn.edu</ext-link>.</corresp>
</author-notes>
<pub-date pub-type="ppub"><year>2023</year></pub-date><pub-date pub-type="epub"><day>25</day><month>7</month><year>2023</year></pub-date><volume>21</volume><issue>3</issue><fpage>538</fpage><lpage>556</lpage><supplementary-material id="S1" content-type="archive" xlink:href="jds1110_s001.zip" mimetype="application" mime-subtype="x-zip-compressed">
<caption>
<title>Supplementary Materials</title>
<p>
<list>
<list-item id="j_jds1110_li_001">
<label>(1)</label>
<p>The code used for benchmarks and the <sans-serif>R Markdown</sans-serif> source for the paper can be found at <uri>https://github.com/Yelie-Yuan/code-sharing/tree/main/generating-pa</uri>.</p>
</list-item>
<list-item id="j_jds1110_li_002">
<label>(2)</label>
<p>The development version of the package is available at <uri>https://gitlab.com/wdnetwork/wdnet</uri>.</p>
</list-item>
</list> 
</p>
</caption>
</supplementary-material><history><date date-type="received"><day>19</day><month>5</month><year>2023</year></date><date date-type="accepted"><day>5</day><month>7</month><year>2023</year></date></history>
<permissions><copyright-statement>2023 The Author(s). Published by the School of Statistics and the Center for Applied Statistics, Renmin University of China.</copyright-statement><copyright-year>2023</copyright-year>
<license license-type="open-access" xlink:href="https://creativecommons.org/licenses/by/4.0/">
<license-p>Open access article under the <ext-link ext-link-type="uri" xlink:href="https://creativecommons.org/licenses/by/4.0/">CC BY</ext-link> license.</license-p></license></permissions>
<abstract>
<p>Preferential attachment (PA) network models have a wide range of applications in various scientific disciplines. Efficient generation of large-scale PA networks helps uncover their structural properties and facilitate the development of associated analytical methodologies. Existing software packages only provide limited functions for this purpose with restricted configurations and efficiency. We present a generic, user-friendly implementation of weighted, directed PA network generation with <sans-serif>R</sans-serif> package <italic>wdnet</italic>. The core algorithm is based on an efficient binary tree approach. The package further allows adding multiple edges at a time, heterogeneous reciprocal edges, and user-specified preference functions. The engine under the hood is implemented in <sans-serif>C++</sans-serif>. Usages of the package are illustrated with detailed explanation. A benchmark study shows that <italic>wdnet</italic> is efficient for generating general PA networks not available in other packages. In restricted settings that can be handled by existing packages, <italic>wdnet</italic> provides comparable efficiency.</p>
</abstract>
<kwd-group>
<label>Keywords</label>
<kwd>complete binary tree</kwd>
<kwd>heterogeneous reciprocity</kwd>
<kwd>multiple addition</kwd>
<kwd>user-specified preference function</kwd>
<kwd>weighted and directed network</kwd>
</kwd-group>
<funding-group><award-group><funding-source xlink:href="https://doi.org/10.13039/501100020414">NSF</funding-source><award-id>DMS2210735</award-id></award-group><funding-statement>Dr. Wang and Dr. Yan’s works were partially supported by the NSF grant DMS2210735. </funding-statement></funding-group>
</article-meta>
</front>
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