update slides

SLIDES/vignette-01-introduction-installation.html

@@ -455,23 +455,33 @@ <h2><span class="r-fit-text">R uses a lot of code from other languages</span></h
 <h2>Lots of people use R</h2>
 <ul>
 <li>Very active community on the web, easy to find solutions (same true of Python, I just prefer R)</li>
+</ul>
+<p><br></p>
+<ul>
 <li>E.g., on Stack Overflow, <a href="https://stackoverflow.com/questions/tagged/r">questions tagged [r]</a> gives (2024-03) 505,118</li>
+</ul>
+<p><br></p>
+<ul>
 <li>This also means that ChatGPT or Google Gemini are quite good at answering questions about R</li>
 </ul>
 </section>
 <section id="r-is-a-scripted-language" class="slide level2">
 <h2>R is a scripted language</h2>
 <ul>
 <li>Interactive</li>
+</ul>
+<p><br></p>
+<ul>
 <li>Allows you to work in real time
 <ul>
 <li>Be careful: what is in memory might involve steps not written down in a script</li>
-<li>If you want to reproduce your steps, it is good to write all the steps down in a script and to test from time to time running using <code>Rscript</code>: this will ensure that all that is required to run is indeed loaded to memory when it needs to, i.e., that it is not already there..</li>
+<li>If you want to reproduce your steps, it is good to write all the steps down in a script and to test from time to time using the command line; see <a href="https://julien-arino.github.io/R-for-modellers/SLIDES/vignette-22-R-command-line.html">Vignette 22</a></li>
 </ul></li>
 </ul>
 </section>
 <section id="similar-to-matlab-and-python.." class="slide level2">
 <h2>Similar to matlab and Python..</h2>
+<p><br></p>
 <p>.. with some differences, of course! Otherwise, where would the fun be? ;)</p>
 </section></section>
 <section>
@@ -482,14 +492,21 @@ <h1>Installing R</h1>
 <section id="the-main-location---cran" class="slide level2">
 <h2>The main location - CRAN</h2>
 <ul>
-<li><p>The <a href="https://cran.r-project.org/">Comprehensive R Archive Network</a> or CRAN is where to go for all official things R</p></li>
-<li><p>To install, select your OS from the main page</p></li>
+<li>The <a href="https://cran.r-project.org/">Comprehensive R Archive Network</a> or CRAN is where to go for all official things R</li>
+</ul>
+<p><br></p>
+<ul>
+<li>To install, select your OS from the main page</li>
 </ul>
 </section>
 <section id="a-note-for-linux-users" class="slide level2">
 <h2>A note for Linux users</h2>
+<p><br></p>
+<ul>
+<li>Often, the version on your distribution is not the most up to date</li>
+</ul>
+<p><br></p>
 <ul>
-<li><p>Often, the version on your distribution is not the most up to date</p></li>
 <li><p>Instructions are on CRAN about setting things up so you have the latest version. For instance,</p>
 <ul>
 <li><a href="https://cran.r-project.org/bin/linux/debian/#secure-apt">Debian</a></li>

SLIDES/vignette-01-introduction-installation.qmd

@@ -50,18 +50,29 @@ tail(rversions::r_versions(), n = 8)
 ## Lots of people use R
 
 - Very active community on the web, easy to find solutions (same true of Python, I just prefer R)
+
+<br>
+
 - E.g., on Stack Overflow, [questions tagged [r]](https://stackoverflow.com/questions/tagged/r) gives (2024-03) 505,118
+
+<br>
+
 - This also means that ChatGPT or Google Gemini are quite good at answering questions about R
 
 ## R is a scripted language
 
 - Interactive
+
+<br>
+
 - Allows you to work in real time
     - Be careful: what is in memory might involve steps not written down in a script
-    - If you want to reproduce your steps, it is good to write all the steps down in a script and to test from time to time running using `Rscript`: this will ensure that all that is required to run is indeed loaded to memory when it needs to, i.e., that it is not already there..
+    - If you want to reproduce your steps, it is good to write all the steps down in a script and to test from time to time using the command line; see [Vignette 22](https://julien-arino.github.io/R-for-modellers/SLIDES/vignette-22-R-command-line.html)
 
 ## Similar to matlab and Python..
 
+<br>
+
 .. with some differences, of course! Otherwise, where would the fun be? ;)
 
 # Installing R
@@ -70,12 +81,18 @@ tail(rversions::r_versions(), n = 8)
 
 - The [Comprehensive R Archive Network](https://cran.r-project.org/) or CRAN is where to go for all official things R
 
+<br>
+
 - To install, select your OS from the main page
 
 ## A note for Linux users
 
+<br>
+
 - Often, the version on your distribution is not the most up to date
 
+<br>
+
 - Instructions are on CRAN about setting things up so you have the latest version. For instance,
 
   - [Debian](https://cran.r-project.org/bin/linux/debian/#secure-apt)

SLIDES/vignette-02-Rstudio-and-friends.html

@@ -362,15 +362,19 @@ <h1>Posit</h1>
 <li><p><a href="https://posit.co/">Posit</a> was formerly called <code>RStudio</code>, like their main product</p></li>
 <li><p>Did a lot of development for <code>R</code>, still do even on the open source side of things</p></li>
 <li><p>For-profit company, sells “pro” versions of its open source products</p></li>
-<li><p>IMOBO: in the process of moving to the “dark side”, trying to ram “pro” versions down your throat</p></li>
+<li><p>IMOBO: in the process of moving to the “dark side”</p></li>
 <li><p>You can completely exist without using the pro versions, though, don’t worry!</p></li>
 </ul>
 </section>
 
 <section id="rstudio" class="title-slide slide level1 center">
 <h1>RStudio</h1>
+<p><br></p>
 <ul>
 <li><a href="https://posit.co/products/open-source/rstudio/">RStudio</a> has become the reference IDE for R</li>
+</ul>
+<p><br></p>
+<ul>
 <li><a href="https://posit.co/download/rstudio-desktop/">Download link</a></li>
 </ul>
 </section>
@@ -379,7 +383,13 @@ <h1>RStudio</h1>
 <h1>RStudio server</h1>
 <ul>
 <li><a href="https://posit.co/products/open-source/rstudio-server/">RStudio server</a>: run RStudio on a Linux server and connect via a web interface</li>
+</ul>
+<p><br></p>
+<ul>
 <li><a href="https://posit.co/download/rstudio-server/">Download link</a></li>
+</ul>
+<p><br></p>
+<ul>
 <li>Note that as far as I can tell, there is no mechanism to auto-update RStudio-server, so you will have to program something or check the site regularly..</li>
 </ul>
 </section>
@@ -388,7 +398,13 @@ <h1>RStudio server</h1>
 <h1>RMarkdown</h1>
 <ul>
 <li>Rmarkdown: markdown that incorporates R commands</li>
+</ul>
+<p><br></p>
+<ul>
 <li>Useful for generating reports in html, pdf or doc, can make slides as well..</li>
+</ul>
+<p><br></p>
+<ul>
 <li>See <a href="https://julien-arino.github.io/R-for-modellers/SLIDES/vignette-13-RMarkdown.html">Vignette 13</a></li>
 </ul>
 </section>
@@ -408,16 +424,25 @@ <h1>Sweave</h1>
 <h1>Quarto</h1>
 <ul>
 <li>Promoted as next-gen version of Sweave/RMarkdown</li>
-<li>Will confess that I have not yet seen why switch in the general case</li>
+</ul>
+<p><br></p>
+<ul>
 <li>These Vignettes are created using Quarto and reveal.js</li>
+</ul>
+<p><br></p>
+<ul>
 <li>See <a href="https://julien-arino.github.io/R-for-modellers/SLIDES/vignette-15-Quarto.html">Vignette 15</a></li>
 </ul>
 </section>
 
 <section id="shiny" class="title-slide slide level1 center">
 <h1>Shiny</h1>
+<p><br></p>
+<ul>
+<li>Shiny: easily create an <em>interactive</em> web page running R code</li>
+</ul>
+<p><br></p>
 <ul>
-<li>Shiny: easily create an interactive web site running R code</li>
 <li>See <a href="https://julien-arino.github.io/R-for-modellers/SLIDES/vignette-16-Shiny.html">Vignette 16</a></li>
 </ul>
 </section>

SLIDES/vignette-02-Rstudio-and-friends.qmd

@@ -28,25 +28,42 @@ format:
 
 - For-profit company, sells "pro" versions of its open source products
 
-- IMOBO: in the process of moving to the "dark side", trying to ram "pro" versions down your throat
+- IMOBO: in the process of moving to the "dark side"
 
 - You can completely exist without using the pro versions, though, don't worry!
 
 # RStudio
 
+<br>
+
 - [RStudio](https://posit.co/products/open-source/rstudio/) has become the reference IDE for R
+
+<br>
+
 - [Download link](https://posit.co/download/rstudio-desktop/)
 
 # RStudio server
 
 - [RStudio server](https://posit.co/products/open-source/rstudio-server/): run RStudio on a Linux server and connect via a web interface
+
+<br>
+
 - [Download link](https://posit.co/download/rstudio-server/)
+
+<br>
+
 - Note that as far as I can tell, there is no mechanism to auto-update RStudio-server, so you will have to program something or check the site regularly..
 
 # RMarkdown
 
 - Rmarkdown: markdown that incorporates R commands
+
+<br>
+
 - Useful for generating reports in html, pdf or doc, can make slides as well..
+
+<br>
+
 - See [Vignette 13](https://julien-arino.github.io/R-for-modellers/SLIDES/vignette-13-RMarkdown.html)
 
 # Sweave
@@ -60,13 +77,23 @@ format:
 # Quarto
 
 - Promoted as next-gen version of Sweave/RMarkdown
-- Will confess that I have not yet seen why switch in the general case
+
+<br>
+
 - These Vignettes are created using Quarto and reveal.js
+
+<br>
+
 - See [Vignette 15](https://julien-arino.github.io/R-for-modellers/SLIDES/vignette-15-Quarto.html)
 
 # Shiny
 
-- Shiny: easily create an interactive web site running R code
+<br>
+
+- Shiny: easily create an *interactive* web page running R code
+
+<br>
+
 - See [Vignette 16](https://julien-arino.github.io/R-for-modellers/SLIDES/vignette-16-Shiny.html)
 
 # Shiny server