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about.html

@@ -300,7 +300,7 @@ <h2 class="anchored" data-anchor-id="utilized-software">Utilized Software</h2>
 <span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a> collate  C.UTF-8</span>
 <span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a> ctype    C.UTF-8</span>
 <span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a> tz       UTC</span>
-<span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a> date     2024-12-07</span>
+<span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a> date     2024-12-10</span>
 <span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a> pandoc   3.4 @ /opt/quarto/bin/tools/ (via rmarkdown)</span>
 <span id="cb2-13"><a href="#cb2-13" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb2-14"><a href="#cb2-14" aria-hidden="true" tabindex="-1"></a>─ Packages ───────────────────────────────────────────────────────────────────</span>

choose_license.html

@@ -348,8 +348,8 @@ <h2 class="anchored" data-anchor-id="a-primer-on-licenses">A Primer on Licenses<
 </div>
 </div>
 <div class="callout-body-container callout-body">
-<p>Some journals offer to publish your article under a Creative Commons license, but still demand an exclusive publishing and distribution license or a copyright assignment from you. This would give them more rights than the readers of the article have through the respective Creative Commons license <span class="citation" data-cites="Rumsey2022">(<a href="#ref-Rumsey2022" role="doc-biblioref">Rumsey &amp; Labastida, 2022</a>)</span> and exceeds by far what is necessary to make publication possible <span class="citation" data-cites="Suber2022">(<a href="#ref-Suber2022" role="doc-biblioref">Suber, 2022</a>)</span>. Consequently, authors should oppose this practice and grant publishers the same rights that every other reader of the article has. If your chosen publisher insists on an exclusive license, you may at least retain the copyright for your figures – follow the guide “Retaining copyright for figures in academic publications to allow easy citation and reuse” by <span class="citation" data-cites="Elson2016">Elson (<a href="#ref-Elson2016" role="doc-biblioref">2016</a>)</span> to learn how to do that.</p>
-<p>If you have published a closed-access paper before, you can consult <a href="https://shareyourpaper.org/">ShareYourPaper</a> for legal options to still make it available free of charge to readers.</p>
+<p>Some journals offer to publish your article under a Creative Commons license, but still demand an exclusive publishing and distribution license or a copyright assignment from you. This would give them more rights than the readers of the article have through the respective Creative Commons license <span class="citation" data-cites="Rumsey2022">(<a href="#ref-Rumsey2022" role="doc-biblioref">Rumsey &amp; Labastida, 2022</a>)</span> and exceeds by far what is necessary to make publication possible <span class="citation" data-cites="Suber2022">(<a href="#ref-Suber2022" role="doc-biblioref">Suber, 2022</a>)</span>. Consequently, authors should oppose this practice and grant publishers the same rights that every other reader of the article has. To facilitate self-archiving, one can also modify the contract with publishers via a rights retention statement <span class="citation" data-cites="UKRN2023">(<a href="#ref-UKRN2023" role="doc-biblioref">UK Reproducibility Network &amp; Eglen, 2023</a>)</span> / author’s addendum <span class="citation" data-cites="SPARC2006">(<a href="#ref-SPARC2006" role="doc-biblioref">SPARC, 2006</a>)</span>. If you have published a closed-access paper before, you can consult <a href="https://shareyourpaper.org/">ShareYourPaper</a> for legal options to still make it available free of charge to readers.</p>
+<p>If your chosen publisher insists on an exclusive license, you may at least retain the copyright for your figures – follow the guide “Retaining copyright for figures in academic publications to allow easy citation and reuse” by <span class="citation" data-cites="Elson2016">Elson (<a href="#ref-Elson2016" role="doc-biblioref">2016</a>)</span> to learn how to do that.</p>
 </div>
 </div>
 <p>The licenses we discuss here mostly regard copyright. Therefore, recipients may lack other rights such as publicity, privacy, moral, patent,<a href="#fn2" class="footnote-ref" id="fnref2" role="doc-noteref"><sup>2</sup></a> or trademark rights. For example, sharing photos that depict people is not only a matter of copyright, but also of privacy rights. Conversely, the licenses do not apply if recipients are allowed to use the works for other reasons such as fair use, the right to quote, or because they made a different arrangement with the author.</p>
@@ -556,7 +556,7 @@ <h2 class="anchored" data-anchor-id="applying-the-license">Applying the License<
 </div>
 </div>
 <div class="callout-body-container callout-body">
-<p>You may have noticed that we mostly refer to licenses using a name <em>and</em> a version number. This is because the organizations that created the licenses sometimes publish updated versions to accommodate for developments in copyright law and the communities that use the licenses. For example, the Creative Commons licenses (that start with <code>CC</code>) were first published in 2002. Since then, the possibility to relicense under later (<a href="https://creativecommons.org/2004/05/25/announcingandexplainingournew20licenses/#:~:text=Share%20Alike%20Across%20Borders">v2.0</a>) and compatible licenses (<a href="https://creativecommons.org/2007/02/23/version-30-launched/">v3.0</a>) has been added, a 30-day window to correct license violations has been established to combat <a href="https://commons.wikimedia.org/wiki/Commons:Copyleft_trolling">copyleft trolls</a>, and <em>sui generis</em> database rights are covered explicitly (<a href="https://creativecommons.org/version4/">v4.0</a>). There are many more <a href="https://wiki.creativecommons.org/wiki/License_Versions">subtle differences between license versions</a>, therefore it is important to indicate which license version exactly one is referring to, as the license of a work does not “update” automatically.</p>
+<p>You may have noticed that we mostly refer to licenses using a name <em>and</em> a version number. This is because the organizations that created the licenses sometimes publish updated versions to accommodate for developments in copyright law and the communities that use the licenses. For example, the Creative Commons licenses (that start with <code>CC</code>) were first published in 2002. Since then, the possibility to relicense under later (<a href="https://creativecommons.org/weblog/entry/4216#:~:text=Share%20Alike%20Across%20Borders">v2.0</a>, 2004) and compatible licenses (<a href="https://creativecommons.org/weblog/entry/7249">v3.0</a>, 2007) has been added, a 30-day window to correct license violations has been established to combat <a href="https://commons.wikimedia.org/wiki/Commons:Copyleft_trolling">copyleft trolls</a>, and <em>sui generis</em> database rights are covered explicitly (<a href="https://creativecommons.org/weblog/entry/40768">v4.0</a>, 2013). There are many more <a href="https://wiki.creativecommons.org/wiki/License_Versions">subtle differences between license versions</a>, therefore it is important to indicate which license version exactly one is referring to, as the license of a work does not “update” automatically. CC0, officially introduced in 2009, is still at version <a href="http://www.creativecommons.org/weblog/entry/13304">1.0</a>.</p>
 <p>For the AGPLv3 it is even recommended to state whether a work is licensed under exactly the indicated version of the license or, alternatively, also under newer versions of the license <span class="citation" data-cites="Stallman2022Version">(<a href="#ref-Stallman2022Version" role="doc-biblioref">Stallman, 2022a</a>)</span>.</p>
 </div>
 </div>
@@ -779,14 +779,14 @@ <h2 class="anchored" data-anchor-id="wrap-up">Wrap-up</h2>
   regulation --"Exists"--&gt; follow_existing_norms["&lt;em&gt;Follow that&lt;/em&gt;"]
   regulation --"Does not&lt;br&gt;exist"--&gt; existing_license_content("Adapting content&lt;br&gt; by others?")
 
-  subgraph "License for individual data entries (content)"
+  subgraph content["&lt;strong&gt;License for content&lt;/strong&gt;"]
   existing_license_content --"No, we created the content&lt;br&gt;entirely by ourselves."--&gt; facts("Entries are facts&lt;br&gt;(like measurements&lt;br&gt;or metadata)?")
   existing_license_content --"Yes, it was&lt;br&gt;shared under a&lt;br&gt;free/open license."--&gt; use_existing_license_content["&lt;em&gt;Use that license&lt;/em&gt;"]
   facts --"Yes"--&gt; cc0_content_metadata["CC0 1.0"]
   facts --"No"--&gt; choose_license["&lt;em&gt;Consult flowchart for&lt;br&gt;software, writing,&lt;br&gt;image, audio, and video&lt;/em&gt;"]
   end
 
-  subgraph "License for combination of data (database)"
+  subgraph database["&lt;strong&gt;License for database&lt;/strong&gt;"]
   choose_license --&gt; switch_license["&lt;em&gt;Depending on&lt;br&gt;content license&lt;/em&gt;"]
   use_existing_license_content --&gt; switch_license
 
@@ -892,6 +892,9 @@ <h2 class="anchored" data-anchor-id="wrap-up">Wrap-up</h2>
 <div id="ref-Rumsey2022" class="csl-entry" role="listitem">
 Rumsey, S., &amp; Labastida, I. (2022, July 25). <em>Exclusive licence to publish – now here’s a thing. <span>Plan S</span></em>. <a href="https://www.coalition-s.org/blog/exclusive-licence-to-publish-now-heres-a-thing/">https://www.coalition-s.org/blog/exclusive-licence-to-publish-now-heres-a-thing/</a>
 </div>
+<div id="ref-SPARC2006" class="csl-entry" role="listitem">
+SPARC. (2006). <em>Author rights: Using the <span>SPARC</span> author addendum</em>. <a href="https://sparcopen.org/our-work/author-rights/brochure-html/">https://sparcopen.org/our-work/author-rights/brochure-html/</a>
+</div>
 <div id="ref-Stallman2022Version" class="csl-entry" role="listitem">
 Stallman, R. (2022a, January 22). <em>For clarity’s sake, please don’t say <span>“licensed under <span>GNU</span> <span>GPL</span> 2”</span>!</em> <a href="https://www.gnu.org/licenses/identify-licenses-clearly.html">https://www.gnu.org/licenses/identify-licenses-clearly.html</a>
 </div>
@@ -901,6 +904,9 @@ <h2 class="anchored" data-anchor-id="wrap-up">Wrap-up</h2>
 <div id="ref-Suber2022" class="csl-entry" role="listitem">
 Suber, P. (2022). Publishing without exclusive rights. <em>The Journal of Electronic Publishing</em>, <em>25</em>(1). <a href="https://doi.org/10.3998/jep.1869">https://doi.org/10.3998/jep.1869</a>
 </div>
+<div id="ref-UKRN2023" class="csl-entry" role="listitem">
+UK Reproducibility Network, &amp; Eglen, S. (2023). <em>Rights retention strategy: A primer from <span>UKRN</span></em>. Open Science Framework. <a href="https://doi.org/10.31219/osf.io/2ajsg">https://doi.org/10.31219/osf.io/2ajsg</a>
+</div>
 <div id="ref-Vezina2020" class="csl-entry" role="listitem">
 Vézina, B. (2020, April 21). <em>Why sharing academic publications under <span>“no derivatives”</span> licenses is misguided. Creative commons</em>. <a href="https://creativecommons.org/2020/04/21/academic-publications-under-no-derivatives-licenses-is-misguided/">https://creativecommons.org/2020/04/21/academic-publications-under-no-derivatives-licenses-is-misguided/</a>
 </div>

intro.html

@@ -240,7 +240,7 @@ <h1 class="title">Introduction</h1>
 <h2 class="anchored" data-anchor-id="the-importance-of-sharing">The Importance of Sharing</h2>
 <p>Suppose you are reading an article about a new imaging method to turn seismological data into subsurface images. The article describes the ideas that went into developing this method and presents a few examples to illustrate its superiority over previous approaches. You got interested and would like to apply this method to your own data. However, with only the article available, it could take months to come up with a working solution, if possible at all. This situation has been put aptly by Buckheit &amp; Donoho <span class="citation" data-cites="Buckheit1995">(<a href="#ref-Buckheit1995" role="doc-biblioref">1995, p. 59</a>)</span>, distilling an idea by the geophysicist Jon Claerbout:</p>
 <blockquote class="blockquote">
-<p>“An article about computational science in a scientific publication is not the scholarship itself, it is merely advertising of the scholarship. The actual scholarship is the complete software development environment and the complete set of instructions which generated the figures.”</p>
+<p>“An article about computational science in a scientific publication is <strong>not</strong> the scholarship itself, it is merely <strong>advertising</strong> of the scholarship. The actual scholarship is the complete software development environment and the complete set of instructions which generated the figures.”</p>
 </blockquote>
 <p>Even when researchers merely apply existing methods (rather than report on a new method), sharing the source code and being transparent about the computational environment is imperative to making their results reproducible <span class="citation" data-cites="Ince2012">(<a href="#ref-Ince2012" role="doc-biblioref">Ince et al., 2012</a>)</span>. By reproducibility, we mean “obtaining consistent results using the same input data; computational steps, methods, and code; and conditions of analysis” <span class="citation" data-cites="NASEM2019">(<a href="#ref-NASEM2019" role="doc-biblioref">National Academies of Sciences, Engineering, and Medicine, 2019, p. 46</a>)</span>.</p>
 </section>