fix citations

2022-03-replication/replication.html

@@ -23,8 +23,8 @@
 </section>
 
 <section>
-<section id="slide-org724979e">
-<h2 id="org724979e">Motivation</h2>
+<section id="slide-org3315257">
+<h2 id="org3315257">Motivation</h2>
 <ul>
 <li>There is a replication crisis in science today</li>
 <li>There are plenty of incentives to publish <b>more</b> papers</li>
@@ -34,16 +34,16 @@
 </ul>
 
 
-<div id="orgad040a9" class="figure">
+<div id="orgaffd63d" class="figure">
 <p><img src="science-fictions-book.jpg" alt="science-fictions-book.jpg" />
 </p>
 </div>
 
 </section>
 </section>
 <section>
-<section id="slide-org5552b0c">
-<h2 id="org5552b0c">Our institutions are implicated</h2>
+<section id="slide-orgd9d44b9">
+<h2 id="orgd9d44b9">Our institutions are implicated</h2>
 <ul>
 <li>Publishers charge outrageous fees for essentially running a web / archive service</li>
 <li>Universities continue to promote staff based on questionable metrics</li>
@@ -56,8 +56,8 @@
 </section>
 </section>
 <section>
-<section id="slide-org4388c47">
-<h2 id="org4388c47">The public are starting not to trust academics</h2>
+<section id="slide-orgc54182a">
+<h2 id="orgc54182a">The public are starting not to trust academics</h2>
 <ul>
 <li>Surprisingly, academics are still respected</li>
 <li>Public trust is not a given and should not be taken for granted</li>
@@ -72,17 +72,17 @@
 </section>
 </section>
 <section>
-<section id="slide-org5013140">
-<h2 id="org5013140">Ideas for improving replicability</h2>
+<section id="slide-org6a6d052">
+<h2 id="org6a6d052">Ideas for improving replicability</h2>
 <p>
 These ideas are focused on the <i>analysis</i> rather than the experimental work itself.
 </p>
 
 </section>
 </section>
 <section>
-<section id="slide-orgd0a3611">
-<h2 id="orgd0a3611">Please stop using Word and Excel</h2>
+<section id="slide-org8c03e15">
+<h2 id="org8c03e15">Please stop using Word and Excel</h2>
 <ul>
 <li>An old version of Excel caused a statistical analysis error during the Covid pandemic
 <ul>
@@ -97,8 +97,8 @@ These ideas are focused on the <i>analysis</i> rather than the experimental work
 </section>
 </section>
 <section>
-<section id="slide-org89d5068">
-<h2 id="org89d5068">Use the command line and GNU Make</h2>
+<section id="slide-orgd3a1778">
+<h2 id="orgd3a1778">Use the command line and GNU Make</h2>
 <ul>
 <li>Analysis ends up having several steps
 <ul>
@@ -115,8 +115,8 @@ These ideas are focused on the <i>analysis</i> rather than the experimental work
 </section>
 </section>
 <section>
-<section id="slide-org6b79784">
-<h2 id="org6b79784">Method for using Make</h2>
+<section id="slide-org01629db">
+<h2 id="org01629db">Method for using Make</h2>
 <ul>
 <li>Each step should be performed with a command or script (e.g., gnuplot)</li>
 <li>Form multiple steps into a pipeline with GNU Make</li>
@@ -129,8 +129,8 @@ These ideas are focused on the <i>analysis</i> rather than the experimental work
 </section>
 </section>
 <section>
-<section id="slide-org41679c5">
-<h2 id="org41679c5">Example&#x2014;generating data</h2>
+<section id="slide-org50d64ad">
+<h2 id="org50d64ad">Example&#x2014;generating data</h2>
 <p>
 For example, say we have a script to generate some data <code>a.csv</code>, <code>b.csv</code>, <code>c.csv</code> called <code>gen.py</code>
 </p>
@@ -154,8 +154,8 @@ df.to_csv(<span style="color: #79a8ff;">"c.csv"</span>, index=<span style="color
 </section>
 </section>
 <section>
-<section id="slide-org3e9772c">
-<h2 id="org3e9772c">Example&#x2014;combine data</h2>
+<section id="slide-org0965c80">
+<h2 id="org0965c80">Example&#x2014;combine data</h2>
 <p>
 We might then have another script <code>comb.py</code> to combine them.
 </p>
@@ -175,8 +175,8 @@ df.to_csv(<span style="color: #79a8ff;">"all.csv"</span>, index=<span style="col
 </section>
 </section>
 <section>
-<section id="slide-orgba68c36">
-<h2 id="orgba68c36">Example&#x2014;table</h2>
+<section id="slide-org477553f">
+<h2 id="org477553f">Example&#x2014;table</h2>
 <p>
 We can produce a table using python tabulate in a script called <code>maketable.py</code>
 </p>
@@ -202,8 +202,8 @@ We can produce a table using python tabulate in a script called <code>maketable.
 </section>
 </section>
 <section>
-<section id="slide-org4e8ee6e">
-<h2 id="org4e8ee6e">Example&#x2014;graph</h2>
+<section id="slide-org12f4bc7">
+<h2 id="org12f4bc7">Example&#x2014;graph</h2>
 <p>
 Finally, we might use <code>graph.py</code> to plot <code>a</code> versus <code>b</code> (ok, this is not a very meaningful graph!)
 </p>
@@ -219,16 +219,16 @@ plt.savefig(<span style="color: #79a8ff;">"graph.png"</span>)
 </div>
 
 
-<div id="org3a1fb3a" class="figure">
+<div id="org8cb57d0" class="figure">
 <p><img src="graph.png" alt="graph.png" />
 </p>
 </div>
 
 </section>
 </section>
 <section>
-<section id="slide-org0eb2f47">
-<h2 id="org0eb2f47">Example&#x2014;LaTeX doc</h2>
+<section id="slide-orgcd1c2d5">
+<h2 id="orgcd1c2d5">Example&#x2014;LaTeX doc</h2>
 <p>
 Naturally, we need a LaTeX document:
 </p>
@@ -256,8 +256,8 @@ Blah blah blah.
 </section>
 </section>
 <section>
-<section id="slide-orgb0c60ec">
-<h2 id="orgb0c60ec">Example&#x2014;Makefile</h2>
+<section id="slide-orgf3f6d59">
+<h2 id="orgf3f6d59">Example&#x2014;Makefile</h2>
 <p>
 Finally, we tie everything together with a <code>Makefile</code>
 </p>
@@ -284,8 +284,8 @@ Finally, we tie everything together with a <code>Makefile</code>
 </section>
 </section>
 <section>
-<section id="slide-org15098e7">
-<h2 id="org15098e7">Using RStudio</h2>
+<section id="slide-orgb407890">
+<h2 id="orgb407890">Using RStudio</h2>
 <ul>
 <li>RStudio allows you to put all the steps into a notebook form</li>
 <li>The result can be exported to a LaTeX document</li>
@@ -297,8 +297,8 @@ Finally, we tie everything together with a <code>Makefile</code>
 </section>
 </section>
 <section>
-<section id="slide-orgbf89696">
-<h2 id="orgbf89696">RStudio example</h2>
+<section id="slide-org77308f4">
+<h2 id="org77308f4">RStudio example</h2>
 <div class="org-src-container">
 
 <pre  class="src src-markdown"   ><code trim>---
@@ -360,8 +360,8 @@ that generated the plot.
 </section>
 </section>
 <section>
-<section id="slide-org0278ec1">
-<h2 id="org0278ec1">Use Jupyter Notebook</h2>
+<section id="slide-org5de2597">
+<h2 id="org5de2597">Use Jupyter Notebook</h2>
 <ul>
 <li>Jupyter notebook supports Python and several other languages</li>
 <li>As with Rstudio, can produce LaTeX by combining code, graphs, and markdown</li>
@@ -372,8 +372,8 @@ that generated the plot.
 </section>
 </section>
 <section>
-<section id="slide-orgdacbc58">
-<h2 id="orgdacbc58">Use Emacs org-mode</h2>
+<section id="slide-org8cb8d12">
+<h2 id="org8cb8d12">Use Emacs org-mode</h2>
 <ul>
 <li>Org mode is a powerful editing environment that comes with Emacs</li>
 <li>Org mode documents are similar to Rmarkdown (or pandoc) with easy formatting instructions</li>
@@ -385,8 +385,8 @@ that generated the plot.
 </section>
 </section>
 <section>
-<section id="slide-orgbfcf58a">
-<h2 id="orgbfcf58a">Using a different latex class</h2>
+<section id="slide-orgda9e82e">
+<h2 id="orgda9e82e">Using a different latex class</h2>
 <ol>
 <li>Your org mode document will need <code>#+latex_class: IEEEtran</code></li>
 <li>You'll need to configure Emacs using something like:</li>
@@ -409,15 +409,22 @@ that generated the plot.
 </section>
 </section>
 <section>
-<section id="slide-orgbabcdb9">
-<h2 id="orgbabcdb9">Further reading</h2>
+<section id="slide-orgc0f65bb">
+<h2 id="orgc0f65bb">Further reading</h2>
 <ol>
-<li>I thoroughly recommend Science Fictions <a href="&amp;ritchieScienceFictionsExposing2020">&amp;ritchieScienceFictionsExposing2020</a></li>
-<li>John Kitchin has a nice article on embedding data into PDFs. <a href="&amp;kitchinExamplesEffectiveData2015">&amp;kitchinExamplesEffectiveData2015</a></li>
+<li>I thoroughly recommend Science Fictions (<a href="#citeproc_bib_item_2">Ritchie, 2020</a>)</li>
+<li>John Kitchin has a nice article on embedding data into PDFs. (<a href="#citeproc_bib_item_1">Kitchin, 2015</a>)</li>
 <li>He also has a youtube describing org mode for research <a href="https://youtu.be/1-dUkyn_fZA">https://youtu.be/1-dUkyn_fZA</a></li>
 
 </ol>
 </section>
+<section id="slide-orgc1ab15e">
+<h3 id="orgc1ab15e">References</h3>
+<div class="csl-bib-body">
+  <div class="csl-entry"><a id="citeproc_bib_item_1"></a>Kitchin, J.R. (2015) “Examples of Effective Data Sharing in Scientific Publishing,” <i>Acs catalysis</i>, 5(6), pp. 3894–3899. Available at: <a href="https://doi.org/10.1021/acscatal.5b00538">https://doi.org/10.1021/acscatal.5b00538</a>.</div>
+  <div class="csl-entry"><a id="citeproc_bib_item_2"></a>Ritchie, S. (2020) <i>Science fictions: Exposing fraud, bias, negligence and hype in science</i>. Random House.</div>
+</div>
+</section>
 </section>
 </div>
 </div>

2022-03-replication/replication.org

@@ -204,13 +204,16 @@ a.csv: gen.py
 
 * Further reading
 
-1. I thoroughly recommend Science Fictions [[cite:&ritchieScienceFictionsExposing2020]]
-2. John Kitchin has a nice article on embedding data into PDFs. [[cite:&kitchinExamplesEffectiveData2015]]
+1. I thoroughly recommend Science Fictions [cite:@ritchieScienceFictionsExposing2020]
+2. John Kitchin has a nice article on embedding data into PDFs. [cite:@kitchinExamplesEffectiveData2015]
 3. He also has a youtube describing org mode for research https://youtu.be/1-dUkyn_fZA
-
-
+** References
+#+print_bibliography:    
+#+bibliography: ~/Documents/zotero-export.bib
+#+CITE_EXPORT: csl ~/Zotero/styles/harvard-cite-them-right.csl
 
 * build :noexport:
 [[elisp:(org-beamer-export-to-pdf)]]
 bibliographystyle:plainnat
 bibliography:~/Documents/zotero-export.bib
+

index.org

@@ -11,4 +11,4 @@
 
 * 2022
 
-[[https://github.coventry.ac.uk/pages/aa3172/presentations/2022-03-replication/replication.pdf][Making your work replicable (2022-03)]]
+[[https://github.coventry.ac.uk/pages/aa3172/presentations/2022-03-replication/replication.html][Making your work replicable (2022-03)]]