fix: replace rmarkdown with quarto resources

docs/references.html

@@ -235,6 +235,10 @@ <h1 class="title"><span id="sec-references" class="quarto-section-identifier">Re
 </header>
 
 <div id="refs" class="references csl-bib-body hanging-indent" role="list">
+<div id="ref-quarto" class="csl-entry" role="listitem">
+Allaire, J. J., Charles Teague, Carlos Scheidegger, Yihui Xie, and
+Christophe Dervieux. 2022. <span>“<span>Quarto</span>.”</span> <a href="https://doi.org/10.5281/zenodo.5960048">https://doi.org/10.5281/zenodo.5960048</a>.
+</div>
 <div id="ref-rmarkdown" class="csl-entry" role="listitem">
 Allaire, JJ, Yihui Xie, Jonathan McPherson, Javier Luraschi, Kevin
 Ushey, Aron Atkins, Hadley Wickham, Joe Cheng, Winston Chang, and

docs/resources.html

@@ -218,7 +218,7 @@ <h2 id="toc-title">Table of contents</h2>
 
   <ul>
   <li><a href="#learning-the-tidyverse" id="toc-learning-the-tidyverse" class="nav-link active" data-scroll-target="#learning-the-tidyverse">Learning the tidyverse</a></li>
-  <li><a href="#learning-rmarkdown-and-quarto" id="toc-learning-rmarkdown-and-quarto" class="nav-link" data-scroll-target="#learning-rmarkdown-and-quarto">Learning Rmarkdown and Quarto</a></li>
+  <li><a href="#learning-quarto" id="toc-learning-quarto" class="nav-link" data-scroll-target="#learning-quarto">Learning Quarto</a></li>
   <li><a href="#learning-r-in-general" id="toc-learning-r-in-general" class="nav-link" data-scroll-target="#learning-r-in-general">Learning R in general</a></li>
   <li><a href="#learning-statistics" id="toc-learning-statistics" class="nav-link" data-scroll-target="#learning-statistics">Learning Statistics</a></li>
   <li><a href="#helpful-tools" id="toc-helpful-tools" class="nav-link" data-scroll-target="#helpful-tools">Helpful tools</a></li>
@@ -264,15 +264,12 @@ <h2 class="anchored" data-anchor-id="learning-the-tidyverse">Learning the tidyve
 <li><a href="https://education.rstudio.com/">RStudio Education</a></li>
 </ul>
 </section>
-<section id="learning-rmarkdown-and-quarto" class="level2">
-<h2 class="anchored" data-anchor-id="learning-rmarkdown-and-quarto">Learning Rmarkdown and Quarto</h2>
+<section id="learning-quarto" class="level2">
+<h2 class="anchored" data-anchor-id="learning-quarto">Learning Quarto</h2>
 <ul>
 <li><a href="https://quarto.org">quarto website</a></li>
-<li><a href="https://rstudio.com/wp-content/uploads/2015/03/rmarkdown-cheatsheet-2.0.pdf">rmarkdown cheatsheet</a></li>
-<li><a href="https://rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf">rmarkdown reference</a></li>
+<li><a href="https://quarto.org/docs/authoring/markdown-basics.html">markdown syntax reference</a></li>
 <li><a href="https://pandoc.org/MANUAL.html#pandocs-markdown">pandoc manual (advanced)</a></li>
-<li><a href="https://reproducible-analysis-workshop.readthedocs.io/en/latest/6.RMarkdown-knitr.html">rmarkdown for reproducible analysis</a></li>
-<li><a href="https://rmarkdown.rstudio.com/index.html">rmarkdown website</a></li>
 </ul>
 </section>
 <section id="learning-r-in-general" class="level2">
@@ -351,8 +348,6 @@ <h2 class="anchored" data-anchor-id="books-and-manuals">Books and Manuals</h2>
 <ul>
 <li><a href="https://www.tmwr.org/">Tidymodels book</a></li>
 <li><a href="https://ggplot2-book.org/">ggplot book</a></li>
-<li><a href="https://bookdown.org/yihui/rmarkdown-cookbook/">Rmarkdown Cookbook</a></li>
-<li><a href="https://bookdown.org/yihui/rmarkdown/">Rmarkdown Book</a></li>
 </ul>
 </section>
 <section id="getting-help" class="level2">
@@ -373,14 +368,18 @@ <h2 class="anchored" data-anchor-id="lists-of-resources">Lists of Resources</h2>
 <section id="packages-that-enable-this-lecture-format" class="level2">
 <h2 class="anchored" data-anchor-id="packages-that-enable-this-lecture-format">Packages that enable this lecture format</h2>
 <ul>
-<li>R by <span class="citation" data-cites="rcoreteamLanguageEnvironmentStatistical2020a">R Core Team (<a href="references.html#ref-rcoreteamLanguageEnvironmentStatistical2020a" role="doc-biblioref">2020</a>)</span></li>
-<li>knitr by <span class="citation" data-cites="knitr">(<a href="references.html#ref-knitr" role="doc-biblioref">Xie 2021</a>)</span></li>
-<li>rmarkdown by <span class="citation" data-cites="rmarkdown">(<a href="references.html#ref-rmarkdown" role="doc-biblioref">Allaire et al. 2021</a>)</span></li>
-<li>xaringan by <span class="citation" data-cites="xieXaringanPresentationNinja2020">Xie (<a href="references.html#ref-xieXaringanPresentationNinja2020" role="doc-biblioref">2020</a>)</span></li>
+<li>R <span class="citation" data-cites="rcoreteamLanguageEnvironmentStatistical2020a">(<a href="references.html#ref-rcoreteamLanguageEnvironmentStatistical2020a" role="doc-biblioref">R Core Team 2020</a>)</span></li>
+<li>Quarto <span class="citation" data-cites="quarto">(<a href="references.html#ref-quarto" role="doc-biblioref">J. J. Allaire et al. 2022</a>)</span></li>
+<li>knitr <span class="citation" data-cites="knitr">(<a href="references.html#ref-knitr" role="doc-biblioref">Xie 2021</a>)</span></li>
+<li>rmarkdown <span class="citation" data-cites="rmarkdown">(<a href="references.html#ref-rmarkdown" role="doc-biblioref">J. Allaire et al. 2021</a>)</span></li>
+<li>xaringan <span class="citation" data-cites="xieXaringanPresentationNinja2020">(<a href="references.html#ref-xieXaringanPresentationNinja2020" role="doc-biblioref">Xie 2020</a>)</span></li>
 </ul>
 
 
 <div id="refs" class="references csl-bib-body hanging-indent" role="list" style="display: none">
+<div id="ref-quarto" class="csl-entry" role="listitem">
+Allaire, J. J., Charles Teague, Carlos Scheidegger, Yihui Xie, and Christophe Dervieux. 2022. <span>“<span>Quarto</span>.”</span> <a href="https://doi.org/10.5281/zenodo.5960048">https://doi.org/10.5281/zenodo.5960048</a>.
+</div>
 <div id="ref-rmarkdown" class="csl-entry" role="listitem">
 Allaire, JJ, Yihui Xie, Jonathan McPherson, Javier Luraschi, Kevin Ushey, Aron Atkins, Hadley Wickham, Joe Cheng, Winston Chang, and Richard Iannone. 2021. <em>Rmarkdown: Dynamic Documents for r</em>. <a href="https://CRAN.R-project.org/package=rmarkdown">https://CRAN.R-project.org/package=rmarkdown</a>.
 </div>

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@@ -571,7 +571,7 @@
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-    "text": "Packages that enable this lecture format\n\nR by R Core Team (2020)\nknitr by (Xie 2021)\nrmarkdown by (Allaire et al. 2021)\nxaringan by Xie (2020)\n\n\n\n\n\nAllaire, JJ, Yihui Xie, Jonathan McPherson, Javier Luraschi, Kevin Ushey, Aron Atkins, Hadley Wickham, Joe Cheng, Winston Chang, and Richard Iannone. 2021. Rmarkdown: Dynamic Documents for r. https://CRAN.R-project.org/package=rmarkdown.\n\n\nChang, Winston. 2013. R Graphics Cookbook: Practical Recipes for Visualizing Data. 1 edition. Beijing Cambridge Farnham Köln Sebastopol Tokyo: O’Reilly Media.\n\n\nGrolemund, Garrett, and Hadley Wickham. 2014. Hands-On Programming with R: Write Your Own Functions and Simulations. Sebastopol, CA: O’Reilly Media.\n\n\nHealy, Kieran. 2018. Data Visualization: A Practical Introduction. 1 edition. Princeton, NJ: Princeton University Press.\n\n\nHorst, Allison. 2020. “Artwork by @Allison_horst.” https://github.com/allisonhorst/stats-illustrations. https://github.com/allisonhorst/stats-illustrations.\n\n\nKim, Chester Ismay and Albert Y. 2019. Statistical Inference via Data Science. CRC Press.\n\n\nMotulsky, Harvey. 2017. Intuitive Biostatistics: A Nonmathematical Guide to Statistical Thinking. 4 edition. New York: Oxford University Press.\n\n\nR Core Team. 2020. R: A Language and Environment for Statistical Computing. Manual. Vienna, Austria: R Foundation for Statistical Computing.\n\n\nReinhart, Alex. 2015. Statistics Done Wrong: The Woefully Complete Guide. 1 edition. San Francisco: No Starch Press.\n\n\nWickham, Hadley. 2015. R Packages: Organize, Test, Document, and Share Your Code. 1 edition. Sebastopol, CA: O’Reilly Media.\n\n\n———. 2019. Advanced R, Second Edition. 2 edition. Boca Raton: Chapman and Hall/CRC.\n\n\nWickham, Hadley, and Garrett Grolemund. 2017. R for Data Science: Import, Tidy, Transform, Visualize, and Model Data. 1 edition. Sebastopol, CA: O’Reilly Media.\n\n\nXie, Yihui. 2020. Xaringan: Presentation Ninja. Manual.\n\n\n———. 2021. Knitr: A General-Purpose Package for Dynamic Report Generation in r. https://yihui.org/knitr/."
+    "text": "Packages that enable this lecture format\n\nR (R Core Team 2020)\nQuarto (J. J. Allaire et al. 2022)\nknitr (Xie 2021)\nrmarkdown (J. Allaire et al. 2021)\nxaringan (Xie 2020)\n\n\n\n\n\nAllaire, J. J., Charles Teague, Carlos Scheidegger, Yihui Xie, and Christophe Dervieux. 2022. “Quarto.” https://doi.org/10.5281/zenodo.5960048.\n\n\nAllaire, JJ, Yihui Xie, Jonathan McPherson, Javier Luraschi, Kevin Ushey, Aron Atkins, Hadley Wickham, Joe Cheng, Winston Chang, and Richard Iannone. 2021. Rmarkdown: Dynamic Documents for r. https://CRAN.R-project.org/package=rmarkdown.\n\n\nChang, Winston. 2013. R Graphics Cookbook: Practical Recipes for Visualizing Data. 1 edition. Beijing Cambridge Farnham Köln Sebastopol Tokyo: O’Reilly Media.\n\n\nGrolemund, Garrett, and Hadley Wickham. 2014. Hands-On Programming with R: Write Your Own Functions and Simulations. Sebastopol, CA: O’Reilly Media.\n\n\nHealy, Kieran. 2018. Data Visualization: A Practical Introduction. 1 edition. Princeton, NJ: Princeton University Press.\n\n\nHorst, Allison. 2020. “Artwork by @Allison_horst.” https://github.com/allisonhorst/stats-illustrations. https://github.com/allisonhorst/stats-illustrations.\n\n\nKim, Chester Ismay and Albert Y. 2019. Statistical Inference via Data Science. CRC Press.\n\n\nMotulsky, Harvey. 2017. Intuitive Biostatistics: A Nonmathematical Guide to Statistical Thinking. 4 edition. New York: Oxford University Press.\n\n\nR Core Team. 2020. R: A Language and Environment for Statistical Computing. Manual. Vienna, Austria: R Foundation for Statistical Computing.\n\n\nReinhart, Alex. 2015. Statistics Done Wrong: The Woefully Complete Guide. 1 edition. San Francisco: No Starch Press.\n\n\nWickham, Hadley. 2015. R Packages: Organize, Test, Document, and Share Your Code. 1 edition. Sebastopol, CA: O’Reilly Media.\n\n\n———. 2019. Advanced R, Second Edition. 2 edition. Boca Raton: Chapman and Hall/CRC.\n\n\nWickham, Hadley, and Garrett Grolemund. 2017. R for Data Science: Import, Tidy, Transform, Visualize, and Model Data. 1 edition. Sebastopol, CA: O’Reilly Media.\n\n\nXie, Yihui. 2020. Xaringan: Presentation Ninja. Manual.\n\n\n———. 2021. Knitr: A General-Purpose Package for Dynamic Report Generation in r. https://yihui.org/knitr/."
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-    "text": "Allaire, JJ, Yihui Xie, Jonathan McPherson, Javier Luraschi, Kevin\nUshey, Aron Atkins, Hadley Wickham, Joe Cheng, Winston Chang, and\nRichard Iannone. 2021. Rmarkdown: Dynamic Documents for r. https://CRAN.R-project.org/package=rmarkdown.\n\n\nBryan, Jennifer. 2017. Gapminder: Data from\nGapminder. Manual.\n\n\nChang, Winston. 2013. R Graphics Cookbook:\nPractical Recipes for Visualizing Data. 1\nedition. Beijing Cambridge Farnham Köln Sebastopol Tokyo:\nO’Reilly Media.\n\n\nCodd, E. F. 1990. The Relational Model for Database Management:\nVersion 2. USA: Addison-Wesley Longman\nPublishing Co., Inc.\n\n\nGrolemund, Garrett, and Hadley Wickham. 2014. Hands-On\nProgramming with R: Write Your Own\nFunctions and Simulations. Sebastopol,\nCA: O’Reilly Media.\n\n\nHealy, Kieran. 2018. Data Visualization: A\nPractical Introduction. 1 edition. Princeton,\nNJ: Princeton University Press.\n\n\nHorst, Allison. 2020. “Artwork by @Allison_horst.”\nhttps://github.com/allisonhorst/stats-illustrations. https://github.com/allisonhorst/stats-illustrations.\n\n\nHorst, Allison, Alison Hill, and Kristen Gorman. 2020.\nPalmerpenguins: Palmer Archipelago (Antarctica) Penguin\nData. Manual.\n\n\nKim, Chester Ismay and Albert Y. 2019. Statistical\nInference via Data Science. CRC\nPress.\n\n\nMatejka, Justin, and George Fitzmaurice. 2017. “The\nDatasaurus Dozen - Same Stats, Different\nGraphs | Autodesk Research.”\nhttps://doi.org/http://dx.doi.org/10.1145/3025453.3025912.\n\n\nMotulsky, Harvey. 2017. Intuitive Biostatistics:\nA Nonmathematical Guide to Statistical\nThinking. 4 edition. New York: Oxford\nUniversity Press.\n\n\nR Core Team. 2020. R: A Language and Environment for\nStatistical Computing. Manual. Vienna, Austria:\nR Foundation for Statistical Computing.\n\n\nReinhart, Alex. 2015. Statistics Done Wrong: The\nWoefully Complete Guide. 1 edition. San\nFrancisco: No Starch Press.\n\n\n“Survivorship Bias.” 2020. Wikipedia, December.\n\n\nWald, Abraham. 1980. “A Reprint of ’A\nMethod of Estimating Plane Vulnerability Based on\nDamage of Survivors.” CRC-432.\nCENTER FOR NAVAL ANALYSES ALEXANDRIA VA OPERATIONS EVALUATION\nGROUP.\n\n\n“Welcome | Ggplot2.” n.d. https://ggplot2-book.org/.\n\n\nWickham, Hadley. 2010. “A Layered Grammar of\nGraphics.” Journal of Computational and\nGraphical Statistics 19 (1): 3–28. https://doi.org/10.1198/jcgs.2009.07098.\n\n\n———. 2014. “Tidy Data.” Journal of\nStatistical Software 59 (1): 1–23. https://doi.org/10.18637/jss.v059.i10.\n\n\n———. 2015. R Packages: Organize,\nTest, Document, and Share Your\nCode. 1 edition. Sebastopol, CA: O’Reilly\nMedia.\n\n\n———. 2016. Ggplot2: Elegant Graphics for Data\nAnalysis. 2nd ed. 2016 edition. New York, NY:\nSpringer.\n\n\n———. 2019. Advanced R, Second\nEdition. 2 edition. Boca Raton: Chapman\nand Hall/CRC.\n\n\nWickham, Hadley, Mara Averick, Jennifer Bryan, Winston Chang, Lucy\nD’Agostino McGowan, Romain François, Garrett Grolemund, et al. 2019.\n“Welcome to the tidyverse.”\nJournal of Open Source Software 4 (43): 1686. https://doi.org/10.21105/joss.01686.\n\n\nWickham, Hadley, and Garrett Grolemund. 2017. R for Data\nScience: Import, Tidy,\nTransform, Visualize, and Model\nData. 1 edition. Sebastopol, CA: O’Reilly\nMedia.\n\n\nWilkinson, Leland, D. Wills, D. Rope, A. Norton, and R. Dubbs. 2005.\nThe Grammar of Graphics. 2nd edition.\nNew York: Springer.\n\n\nWilliams, Timothy. n.d. “The Complexity of\nEvil.” Rutgers University Press.\n\n\nXie, Yihui. 2020. Xaringan: Presentation Ninja.\nManual.\n\n\n———. 2021. Knitr: A General-Purpose Package for Dynamic Report\nGeneration in r. https://yihui.org/knitr/.\n\n\nZiemann, Mark, Yotam Eren, and Assam El-Osta. 2016. “Gene Name\nErrors Are Widespread in the Scientific Literature.” Genome\nBiology 17 (1): 177. https://doi.org/10.1186/s13059-016-1044-7."
+    "text": "Allaire, J. J., Charles Teague, Carlos Scheidegger, Yihui Xie, and\nChristophe Dervieux. 2022. “Quarto.” https://doi.org/10.5281/zenodo.5960048.\n\n\nAllaire, JJ, Yihui Xie, Jonathan McPherson, Javier Luraschi, Kevin\nUshey, Aron Atkins, Hadley Wickham, Joe Cheng, Winston Chang, and\nRichard Iannone. 2021. Rmarkdown: Dynamic Documents for r. https://CRAN.R-project.org/package=rmarkdown.\n\n\nBryan, Jennifer. 2017. Gapminder: Data from\nGapminder. Manual.\n\n\nChang, Winston. 2013. R Graphics Cookbook:\nPractical Recipes for Visualizing Data. 1\nedition. Beijing Cambridge Farnham Köln Sebastopol Tokyo:\nO’Reilly Media.\n\n\nCodd, E. F. 1990. The Relational Model for Database Management:\nVersion 2. USA: Addison-Wesley Longman\nPublishing Co., Inc.\n\n\nGrolemund, Garrett, and Hadley Wickham. 2014. Hands-On\nProgramming with R: Write Your Own\nFunctions and Simulations. Sebastopol,\nCA: O’Reilly Media.\n\n\nHealy, Kieran. 2018. Data Visualization: A\nPractical Introduction. 1 edition. Princeton,\nNJ: Princeton University Press.\n\n\nHorst, Allison. 2020. “Artwork by @Allison_horst.”\nhttps://github.com/allisonhorst/stats-illustrations. https://github.com/allisonhorst/stats-illustrations.\n\n\nHorst, Allison, Alison Hill, and Kristen Gorman. 2020.\nPalmerpenguins: Palmer Archipelago (Antarctica) Penguin\nData. Manual.\n\n\nKim, Chester Ismay and Albert Y. 2019. Statistical\nInference via Data Science. CRC\nPress.\n\n\nMatejka, Justin, and George Fitzmaurice. 2017. “The\nDatasaurus Dozen - Same Stats, Different\nGraphs | Autodesk Research.”\nhttps://doi.org/http://dx.doi.org/10.1145/3025453.3025912.\n\n\nMotulsky, Harvey. 2017. Intuitive Biostatistics:\nA Nonmathematical Guide to Statistical\nThinking. 4 edition. New York: Oxford\nUniversity Press.\n\n\nR Core Team. 2020. R: A Language and Environment for\nStatistical Computing. Manual. Vienna, Austria:\nR Foundation for Statistical Computing.\n\n\nReinhart, Alex. 2015. Statistics Done Wrong: The\nWoefully Complete Guide. 1 edition. San\nFrancisco: No Starch Press.\n\n\n“Survivorship Bias.” 2020. Wikipedia, December.\n\n\nWald, Abraham. 1980. “A Reprint of ’A\nMethod of Estimating Plane Vulnerability Based on\nDamage of Survivors.” CRC-432.\nCENTER FOR NAVAL ANALYSES ALEXANDRIA VA OPERATIONS EVALUATION\nGROUP.\n\n\n“Welcome | Ggplot2.” n.d. https://ggplot2-book.org/.\n\n\nWickham, Hadley. 2010. “A Layered Grammar of\nGraphics.” Journal of Computational and\nGraphical Statistics 19 (1): 3–28. https://doi.org/10.1198/jcgs.2009.07098.\n\n\n———. 2014. “Tidy Data.” Journal of\nStatistical Software 59 (1): 1–23. https://doi.org/10.18637/jss.v059.i10.\n\n\n———. 2015. R Packages: Organize,\nTest, Document, and Share Your\nCode. 1 edition. Sebastopol, CA: O’Reilly\nMedia.\n\n\n———. 2016. Ggplot2: Elegant Graphics for Data\nAnalysis. 2nd ed. 2016 edition. New York, NY:\nSpringer.\n\n\n———. 2019. Advanced R, Second\nEdition. 2 edition. Boca Raton: Chapman\nand Hall/CRC.\n\n\nWickham, Hadley, Mara Averick, Jennifer Bryan, Winston Chang, Lucy\nD’Agostino McGowan, Romain François, Garrett Grolemund, et al. 2019.\n“Welcome to the tidyverse.”\nJournal of Open Source Software 4 (43): 1686. https://doi.org/10.21105/joss.01686.\n\n\nWickham, Hadley, and Garrett Grolemund. 2017. R for Data\nScience: Import, Tidy,\nTransform, Visualize, and Model\nData. 1 edition. Sebastopol, CA: O’Reilly\nMedia.\n\n\nWilkinson, Leland, D. Wills, D. Rope, A. Norton, and R. Dubbs. 2005.\nThe Grammar of Graphics. 2nd edition.\nNew York: Springer.\n\n\nWilliams, Timothy. n.d. “The Complexity of\nEvil.” Rutgers University Press.\n\n\nXie, Yihui. 2020. Xaringan: Presentation Ninja.\nManual.\n\n\n———. 2021. Knitr: A General-Purpose Package for Dynamic Report\nGeneration in r. https://yihui.org/knitr/.\n\n\nZiemann, Mark, Yotam Eren, and Assam El-Osta. 2016. “Gene Name\nErrors Are Widespread in the Scientific Literature.” Genome\nBiology 17 (1): 177. https://doi.org/10.1186/s13059-016-1044-7."
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