varia

Author: zoometh

teach/stats/r4a/2025/index-part1.qmd

@@ -1,5 +1,6 @@
 ---
-title: "Authoring, writing and publishing with<br>R Markdown - part 1"
+title: "Authoring, writing and publishing with R Markdown"
+subtitle: "part 1: Basics and Markdown syntax"
 author: "Thomas Huet, University of Oxford, CNRS-IRAMAT "
 title-slide-attributes:
     data-background-image: "https://raw.githubusercontent.com/zoometh/thomashuet/master/teach/www/logo.png"

teach/stats/r4a/2025/index-part2.qmd

@@ -1,6 +1,6 @@
 ---
 title: "Authoring, writing and publishing with R Markdown"
-subtitle: "part 2: code and YAML header"
+subtitle: "part 2: Advanced R and YAML code integration"
 author: "Thomas Huet, University of Oxford, CNRS-IRAMAT"
 title-slide-attributes:
     data-background-image: "https://raw.githubusercontent.com/zoometh/thomashuet/master/teach/www/logo.png"
@@ -22,7 +22,7 @@ format:
     preview-links: auto
     reference-location: document
     footnotes-hover: true
-    logo: https://raw.githubusercontent.com/zoometh/thomashuet/master/teach/www/inst-uni-oxford_.png
+    logo: https://raw.githubusercontent.com/zoometh/thomashuet/master/img/inst-uni-oxford_cnrs-iramat.png
     # css: ../styles.css
     # css: https://zoometh.github.io/thomashuet/teach/stats/r4a/styles.css
     css: https://zoometh.github.io/thomashuet/css/quarto.css
@@ -33,6 +33,7 @@ pagetitle: "Report with R Markdown - part 2"
 footer: "Report with R Markdown - R4Rchaeologists <img src='https://raw.githubusercontent.com/zoometh/thomashuet/master/teach/www/logo.png' style='height: 35px;vertical-align: middle;'> Università di Pisa, Jan 2025 - <em>presented by </em> Thomas Huet"
 ---
 
+# Code chunks
 
 ## Code chunks {#chunks}
 
@@ -172,11 +173,11 @@ knitr::opts_chunk$set(echo = TRUE)
 <tbody>
   <tr>
     <td>`include = FALSE`</td>
-    <td>prevents `code` and `results` from appearing in the rendered file. R Markdown still runs the code in the chunk, and the results can be used by other chunks.</td>
+    <td>prevents `code` and `output` from appearing in the rendered file. R Markdown still runs the code in the chunk, and the output can be used by other chunks.</td>
   </tr>
   <tr>
     <td>`echo = FALSE`</td>
-    <td>prevents `code`, but not the results from appearing in the rendered file.</td>
+    <td>prevents `code`, but not the output, from appearing in the rendered file.</td>
   </tr>
   <tr>
     <td>`message = FALSE`</td>
@@ -196,7 +197,7 @@ knitr::opts_chunk$set(echo = TRUE)
 <div class="div-code"> 
 <small>code chunk</small>
 ```{.r }
-{r munsingenspat, fig.height = 10, fig.with = 10}
+{r munsingenspat, fig.cap = "my caption", fig.height = 10, fig.with = 10}
 ```
 </div>
 
@@ -212,7 +213,7 @@ knitr::opts_chunk$set(echo = TRUE)
 <tbody>
   <tr>
     <td>`fig.cap = "..."`</td>
-    <td> adds a caption to graphical results.</td>
+    <td> adds a caption to graphical output.</td>
   </tr>
   <tr>
     <td>`fig.height = 7`</td>
@@ -281,6 +282,8 @@ knitr::include_graphics(fibula)
 
 \
 
+# YAML
+
 
 ## YAML {#yaml}
 
@@ -304,7 +307,7 @@ date: '2023-02-05'
 
 \
 
-## YAML dates
+## Dates
 
 <div class="div-yaml"> 
 <small>header YAML</small>
@@ -338,7 +341,7 @@ Here the <notes>`</notes> quote has been changed to a <notes>'</notes> quote for
 :::
 \
 
-## YAML output
+## Output
 
 <span class="r-md">R Markdown</span> output format.
 
@@ -354,14 +357,14 @@ output:
 ```
 </div>
 
-Here a PDF: <small><https://github.com/zoometh/thomashuet/blob/main/teach/stats/r4a/2025/temp.pdf></small>
+<small>Here a PDF: <https://github.com/zoometh/thomashuet/blob/main/teach/stats/r4a/2025/temp.pdf></small>
 
 ```{=html}
 <script src="https://gist.github.com/zoometh/d1b4945d1c16f853a7888ede03c4807d.js"></script>
 ```
 
 
-## YAML table of content
+## Table of content
 
 Table of content (TOC).  
 
@@ -384,7 +387,7 @@ output:
 
 
 
-## YAML references
+## References
 
 Locate the bibliographic file (e.g.  [`references.bib`](https://github.com/zoometh/thomashuet/blob/main/teach/stats/r4a/2025/references.bib)).
 
@@ -411,6 +414,9 @@ see [Xie <em>et al.</em>](https://bookdown.org/yihui/rmarkdown/html-document.htm
 
 \
 
+# More HTML
+
+
 ## Styling
 
 ::: {.panel-tabset}
@@ -544,6 +550,9 @@ Customize with CSS like this <notes>**dodgerblue** background</notes>.
 
 :::
 
+# Advanced publishing
+
+
 ## Interactivity
 
 ::: {.panel-tabset}
@@ -560,7 +569,7 @@ runtime: shiny
 </div>        
         
 ::: {.callout-note}
-Try: `File > New File > Rmarkdown > Shiny`, or in the <span class="r-yaml">YAML header</span>. There are different ways to use <img src='https://raw.githubusercontent.com/zoometh/thomashuet/master/img/app-prg-r-pkg-shiny.png' style='height: 45px;vertical-align: middle;'> in <span class="r-md">R Markdown</span>, for example by embedding an <img src='https://raw.githubusercontent.com/zoometh/thomashuet/master/img/app-prg-html.png' style='height: 45px;vertical-align: middle;'> widget created by Shiny outside the R Markdown document, or by embedding the Shiny coding directly.
+Try: `File > New File > Rmarkdown > Shiny`, or in the <span class="r-yaml">YAML header</span>. There are different ways to use <img src='https://raw.githubusercontent.com/zoometh/thomashuet/master/img/r-pkg-shiny.png' style='height: 45px;vertical-align: middle;'> in <span class="r-md">R Markdown</span>, for example by embedding an <img src='https://raw.githubusercontent.com/zoometh/thomashuet/master/img/app-prg-html.png' style='height: 45px;vertical-align: middle;'> widget created by Shiny outside the R Markdown document, or by embedding the Shiny coding directly.
 ::: 
 \
 
@@ -645,6 +654,10 @@ output: html_document
 
 ## PDF
 
+::: {.panel-tabset}
+
+### Basic
+
 <div class="div-yaml"> 
 <small>header YAML</small>
 ```{.md code-line-numbers="4"}
@@ -658,9 +671,10 @@ output: pdf_document
 
 
 ::: {.callout-note}
-For advanced editing, read below ⬇️
+For advanced editing, read the other tab panel ️➡️
 ::: 
 
+### Advanced
 
 <img src='https://raw.githubusercontent.com/zoometh/thomashuet/master/img/r-pkg-bookdown.png' style='height: 70px;vertical-align: middle;'> is useful in <span class="r-md">R Markdown</span> for chunk calls, and more generally for cross-referencing. <img src='https://raw.githubusercontent.com/zoometh/thomashuet/master/img/app-pao-adobe-pdf.png' style='height: 45px;vertical-align: middle;'> uses <img src='https://raw.githubusercontent.com/zoometh/thomashuet/master/img/app-pao-latex.png' style='height: 45px;vertical-align: middle;'> syntax, if you don't have [MiKTeX](https://miktex.org/) installed, you need to install the <img src="https://raw.githubusercontent.com/zoometh/thomashuet/master/img/r-pkg-tinytex.png" style="height: 70px;vertical-align: middle;"/> package [@Xie19].
 
@@ -698,6 +712,8 @@ These temporary files are creates:
 
 At the end of the rendering, these files are deleted.
 
+:::
+
 \
 
 ## LaTeX
@@ -729,7 +745,7 @@ On <img src="https://raw.githubusercontent.com/zoometh/thomashuet/master/img/app
 
 
 ```{=html}
-<iframe width="1000" height="400" src="https://rpubs.com/"></iframe>
+<iframe width="1000" height="300" src="https://rpubs.com/"></iframe>
 ```
 <small><https://rpubs.com/></small>
 
@@ -776,16 +792,12 @@ On GitHub <img src="https://raw.githubusercontent.com/zoometh/thomashuet/master/
 
 ### Objective
 
-<small>
-
 Use <span class="r-md">R Markdown</span> (<span class="r-code">code chunks</span> and <span class="r-text">narrative parts</span>) to create a report. Choose between:
 
-- [ ] improve the `.Rmd` document: "Münsingen-Rain necropolis (Bern, Switzerland). A quantative study of Late Iron Age fibulae" <img src='https://raw.githubusercontent.com/zoometh/thomashuet/master/teach/www/munsingen_fib_measures.png' style='height: 65px;vertical-align: middle;'> using the dataset 'Fibulae' from {`archdata`} 
+- [ ] improve the `.Rmd` document: "*Münsingen-Rain necropolis (Bern, Switzerland). A quantative study of Late Iron Age fibulae*" using the dataset 'Fibulae' from {`archdata`} 
 
 - [ ] start from scratch ([here](https://zoometh.github.io/thomashuet/teach/stats/r4a/2025/site/index-part1#/new-document)) and select another dataset from {`archdata`} (e.g. 'Handaxes').
 
-</small>
-
 ::: {.callout-note}
 The practical part has an estimated duration of 60 minutes
 :::
@@ -794,30 +806,25 @@ The practical part has an estimated duration of 60 minutes
 
 ### How to start?
 
-<small>Download/Copy the folder `r4a/2025/practice/` and locate the file `2_Rmarkdown_Practice.Rmd` and the .`bib` file by following this link: </small>
+1. Download/Copy the folder `r4a/2025/practice/` and locate the file `2_Rmarkdown_Practice.Rmd` and the .`bib` file by following this link:
 
 ```{.html}
 https://github.com/zoometh/thomashuet/tree/main/teach/stats/r4a/2025/practice/
 ```
 
-<small> You can also use this website to download the folder: </small>
+2. install the {`bookdown`} package
 
-```{=html}
-<iframe width="1000" height="200" src="https://download-directory.github.io/"></iframe>
+```{.r}
+install.packages("bookdown")
 ```
-<small><https://download-directory.github.io/></small>
-
-\
-\
-
 
-### How to end?
+### How to finish?
 
 Contact me, send me your `.Rmd` and related files (e.g. `references.bib`) here online 👋 
 
 <center>or</center>
 
-<img src='https://raw.githubusercontent.com/zoometh/thomashuet/master/img/app-github.png' style='height: 50px;vertical-align: middle;'> <https://github.com/zoometh/thomashuet/issues/2>
+Write a <img src='https://raw.githubusercontent.com/zoometh/thomashuet/master/img/app-github.png' style='height: 50px;vertical-align: middle;'> issue:  <https://github.com/zoometh/thomashuet/issues/2>