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| --- | |
| title: "Write your Dynamic Documents" | |
| author: "Sau-Chin Chen, Tobias Heycke" | |
| date: "2019/2/7" | |
| output: | |
| revealjs::revealjs_presentation: | |
| theme: white | |
| incremental: true | |
| mathjax: local | |
| fig_caption: true | |
| self_contained: false | |
| reveal_plugins: ["zoom"] | |
| --- | |
| ## Before we start | |
| - [R](https://www.r-project.org/) | |
| - [Rstudio](https://www.rstudio.com/) | |
| - (Optional) [Git](https://git-scm.com/),[pandoc](https://pandoc.org/installing.html),[Zotero](https://www.zotero.org/download/) | |
| - Download the [example files](https://github.com/SCgeeker/WS_dynamic_doc/archive/master.zip) | |
| ## Overview | |
| |Input<br>Format|Content|Render|Output<br>Format| | |
| |---|---------|----------|------| | |
| |.md |text<br>markdown tags<br>latex codes<br>citation key|pandoc<br>pandoc-citeproc|.html<br>.pdf<br>.docx | | |
| |.Rmd |code chunks<br>inline codes|rmarkdown |.html<br>.pdf<br>.docx | | |
| |Templates<br>(e.g., APA)|footnote<br>appendix doc|papaja|.pdf| | |
| ## Resource | |
| [R Markdown: The Definitive Guide](https://bookdown.org/yihui/rmarkdown/) | |
| [papaja: Reproducible APA manuscripts with R Markdown](https://crsh.github.io/papaja_man/) | |
| # Markdown | |
| ## | |
| **Example Materials**:<br> `markdown_demo.md`<br>`markdown_demo.bib`<br>`Workshop-Open-Science1.png` | |
| ## Preparation | |
| - [markdown cheatsheet](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet) | |
| - off-line editor | |
| - any text editor | |
| - Rstudio | |
| - render: [pandoc](http://pandoc.org/), [installation guide](https://pandoc.org/installing.html) | |
| - (Optional)Version Control tool: [Git](https://git-scm.com/) | |
| ## Tips | |
| - Keep your text as 'clean' as you can. | |
| - Leave typesetting to *markdown tags*, *Latex codes* | |
| - Organize the bibliography in [Zotero](http://zotero.org/) | |
| # Rmarkdown | |
| ## | |
| **Example Materials**:<br> `Rmd_demo.md`<br>`Orientation Cross Languages.bib`<br>`Lab-summary.csv` | |
| ## Preparation | |
| - [R](https://www.r-project.org/) | |
| - [Rstudio](https://www.rstudio.com/) | |
| - [knitr package](https://cran.r-project.org/web/packages/knitr/index.html) | |
| - bibtext file(s) | |
| - [Rstudio addin: citr](https://github.com/crsh/citr) | |
| ## Setup of sweave | |
|  | |
| ## Tips | |
| - in text -> in table -> in figure | |
| - Import the analytical data at beginning. | |
| - If statistical models take time, it is better to summarize them prior to organize them in chunks. | |
| - If it is workable, making of tables and figures by codes is better than the external files. | |
| # papaja | |
| ## | |
| **Example Materials**:<br> `papaja_appendix_test.zip` | |
| ## Preparation | |
| - TeX distribution | |
| - [TinyTex](https://yihui.name/tinytex/) | |
| - [MikTeX](http://miktex.org/) for Windows ([installation guide]((https://tobiasheycke.github.io/pages/fullmiktex)) by Tobias) | |
| - [MacTeX](https://tug.org/mactex/) for Mac | |
| - [TeX Live](http://www.tug.org/texlive/) for Linux | |
| - papaja package | |
| - [installing commands](https://crsh.github.io/papaja_man/introduction.html#installing-papaja) | |
| ## Tips | |
| - Full TeX distribution installation before your first `papaja` article. | |
| - Manage "Title page" and "Abstract" in YAML. | |
| - Prepare your bibliography file and citation style while writing paper. Set them up in YAML([Guide by Frederik](https://crsh.github.io/papaja_man/writing.html#citations) ). | |
| - Check .tex file(s) when you don't get what you want. | |
| - `papaja` is under development. Search the solutions and submit your questions at [Github](https://github.com/crsh/papaja/issues). | |
| ## Append appendices to manuscript | |
|  | |
| ## Append appendices to manuscript | |
|  |