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‎teach/stats/r4a/2025/index-part2.qmd

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width: 1200
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bibliography: references.bib
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pagetitle: "Report with R Markdown - part 2"
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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, Feb 2024 - <em>presented by </em> Thomas Huet"
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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"
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---
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### Headers options
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Options are used to show/hide the code, change the size and set the alignment of the ouptut, etc.
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<div class="div-code">
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<small>code chunk</small>
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```{.r }
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{r munsingenspat, echo = TRUE, warning = FALSE, message = FALSE}
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```
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</div>
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Options are used to show/hide the code, change the size of the output image, set the alignment of the ouptut, etc.
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<center>
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![](https://raw.githubusercontent.com/zoometh/thomashuet/master/teach/www/rmd_create_rmd_new.png){width="900px"}
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</center>
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<small><https://github.com/zoometh/thomashuet/blob/main/teach/stats/r4a/2024/temp.pdf></small>
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<small><https://github.com/zoometh/thomashuet/blob/main/teach/stats/r4a/2025/temp.pdf></small>
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### Options hierarchy
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The top chunk of the `.Rmd` file is commonly used to set global options for all subsequent chunks, unless you override these options locally within the headers of individual code chunks.
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<div class="div-code">
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<small>code chunk</small>
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```{.r }
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```
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</div>
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The top chunk of the `.Rmd` file is commonly used to set global options for all subsequent chunks, unless you override these options locally within the headers of individual code chunks.
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```{=html}
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<script src="https://gist.github.com/zoometh/d1b4945d1c16f853a7888ede03c4807d.js"></script>
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## YAML {#yaml}
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The <span class="r-yaml">YAML header</span> is the <span class="r-md">R Markdown</span> document header, it contains the metadata (e.g, title), the document output format (e.g, PDF) and configuration (e.g. table of content). It is composed on **key - value** pairs:
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<div class="div-yaml">
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<small>header YAML</small>
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```{.yml}
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```
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</div>
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<span class="r-yaml">YAML header</span> is the document header, it contains the metadata (e.g, title), the document output format (e.g, PDF) and configuration (e.g. table of content). It is composed on **key - value** pairs:
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```{=html}
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<script src="https://gist.github.com/zoometh/d1b4945d1c16f853a7888ede03c4807d.js"></script>
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\
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## YAML output
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<span class="r-md">R Markdown</span> output format.
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<div class="div-yaml">
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<small>header YAML</small>
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```
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</div>
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Select the output format, here a PDF: <small><https://github.com/zoometh/thomashuet/blob/main/teach/stats/r4a/2024/temp.pdf></small>
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Here a PDF: <small><https://github.com/zoometh/thomashuet/blob/main/teach/stats/r4a/2025/temp.pdf></small>
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```{=html}
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<script src="https://gist.github.com/zoometh/d1b4945d1c16f853a7888ede03c4807d.js"></script>
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## YAML table of content
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Table of content (TOC)
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Table of content (TOC).
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<div class="div-yaml">
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<small>header YAML</small>
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## YAML references
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Locate the bibliographic file (e.g. [`references.bib`](https://github.com/zoometh/thomashuet/blob/main/teach/stats/r4a/2025/references.bib)).
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<div class="div-yaml">
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<small>header YAML</small>
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```{.yml code-line-numbers="5"}
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```
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</div>
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Reference the bibliographic file (e.g. [`references.bib`](https://github.com/zoometh/thomashuet/blob/main/teach/stats/r4a/2024/references.bib)). Here in the same folder as the `.Rmd` file.
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Here in the same folder as the `.Rmd` file.
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```{=html}
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:::
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## HTML online editor
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## HTML online editor {data-visibility=hidden}
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::: {.panel-tabset}
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### Shiny
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<img src='https://raw.githubusercontent.com/zoometh/thomashuet/master/img/app-prg-r-pkg-shiny.png' style='height: 45px;vertical-align: middle;'> offers a framework to create interactive documents
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Interactivity with the <img src='https://raw.githubusercontent.com/zoometh/thomashuet/master/img/app-prg-js.png' style='height: 45px;vertical-align: middle;'> package (for the client-side) <img src='https://raw.githubusercontent.com/zoometh/thomashuet/master/img/r-pkg-shiny.png' style='height: 45px;vertical-align: middle;'>
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<div class="div-yaml">
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<small>header YAML</small>
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<tbody>
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<tr>
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<td>raw</td>
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<td><small><https://raw.githubusercontent.com/zoometh/thomashuet/main/teach/stats/r4a/2024/practice/2_Rmarkdown_Practice.Rmd></small></td>
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<td><small><https://raw.githubusercontent.com/zoometh/thomashuet/main/teach/stats/r4a/2025/practice/2_Rmarkdown_Practice.Rmd></small></td>
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</tr>
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<tr>
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<td>`.Rmd`</td>
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<td><small><https://github.com/zoometh/thomashuet/blob/main/teach/stats/r4a/2024/practice/2_Rmarkdown_Practice.Rmd></small></td>
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<td><small><https://github.com/zoometh/thomashuet/blob/main/teach/stats/r4a/2025/practice/2_Rmarkdown_Practice.Rmd></small></td>
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</tr>
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<td>PDF</td>
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<td><small><https://github.com/zoometh/thomashuet/blob/main/teach/stats/r4a/2024/practice/2_Rmarkdown_Practice.pdf></small></td>
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<td><small><https://github.com/zoometh/thomashuet/blob/main/teach/stats/r4a/2025/practice/2_Rmarkdown_Practice.pdf></small></td>
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</tbody>
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\
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\
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:::
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# Practice
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## Practice {#practice}
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::: {.panel-tabset}
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### Objective
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::: {.callout-note}
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The practical part has an estimated duration of 60 minutes
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:::
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<small>
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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:
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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. Choice between:
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- [ ] 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`}
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- [ ] start from scratch ([here](https://zoometh.github.io/thomashuet/teach/stats/r4a/2024/site/index-part1#/new-document))
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- [ ] 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').
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- [ ] improvement of the existing `.Rmd` model for the <img src='https://raw.githubusercontent.com/zoometh/thomashuet/master/teach/www/munsingen_fib_measures.png' style='height: 65px;vertical-align: middle;'> fibulae from the Münsingen cemetery
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</small>
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- [ ] select another dataset from the {`archdata`} package (e.g. 'Handaxes'), to improve the `.Rmd` template
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::: {.callout-note}
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The practical part has an estimated duration of 60 minutes
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:::
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\
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### Data
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### How to start?
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<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>
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Download the folder `r4a/2024/practice/` and locate the file `2_Rmarkdown_Practice.Rmd`:
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```{.html}
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https://github.com/zoometh/thomashuet/tree/main/teach/stats/r4a/2024/practice/
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https://github.com/zoometh/thomashuet/tree/main/teach/stats/r4a/2025/practice/
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```
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You can use this website:
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<small> You can also use this website to download the folder: </small>
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```{=html}
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<iframe width="1000" height="200" src="https://download-directory.github.io/"></iframe>
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```
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<small><https://download-directory.github.io/></small>
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or go here: [https://github.com/zoometh/thomashuet/blob/main/teach/stats/r4a/2024/practice/2_Rmarkdown_Practice.Rmd](https://github.com/zoometh/thomashuet/tree/main/teach/stats/r4a/2024) and download, or copy/paste this `.Rmd` file and the .`bib` file.
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### Output
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### How to end?
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Contact me, send me your `.Rmd`, connected files (e.g. `references.bib`) here 👋 online
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Contact me, send me your `.Rmd` and related files (e.g. `references.bib`) here online 👋
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<center>or</center>
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