Introduction to Rmarkdown

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# .text-shadow[.black[Introduction to Rmarkdown]]
 
### .text-shadow[.white[ &nbsp;Dr Kristy Robledo <svg viewBox="0 0 512 512" style="height:1em;position:relative;display:inline-block;top:.1em;fill:blue;" xmlns="http://www.w3.org/2000/svg"> <path d="M459.37 151.716c.325 4.548.325 9.097.325 13.645 0 138.72-105.583 298.558-298.558 298.558-59.452 0-114.68-17.219-161.137-47.106 8.447.974 16.568 1.299 25.34 1.299 49.055 0 94.213-16.568 130.274-44.832-46.132-.975-84.792-31.188-98.112-72.772 6.498.974 12.995 1.624 19.818 1.624 9.421 0 18.843-1.3 27.614-3.573-48.081-9.747-84.143-51.98-84.143-102.985v-1.299c13.969 7.797 30.214 12.67 47.431 13.319-28.264-18.843-46.781-51.005-46.781-87.391 0-19.492 5.197-37.36 14.294-52.954 51.655 63.675 129.3 105.258 216.365 109.807-1.624-7.797-2.599-15.918-2.599-24.04 0-57.828 46.782-104.934 104.934-104.934 30.213 0 57.502 12.67 76.67 33.137 23.715-4.548 46.456-13.32 66.599-25.34-7.798 24.366-24.366 44.833-46.132 57.827 21.117-2.273 41.584-8.122 60.426-16.243-14.292 20.791-32.161 39.308-52.628 54.253z"></path></svg> @kristyrobledo]]
---
class: center

# .brand-red[RECAP: What can Stata do?]

.center[
<img src="assets/recap.jfif" height=200>
]

[Slides here](https://github.com/kristyrobledo/Intro_Rmarkdown/blob/main/STATA/ACTA%20STInG%20Stata%20Workshop_15022023_Anurika%20De%20Silva.pdf)

[Code here](https://github.com/kristyrobledo/Intro_Rmarkdown/tree/main/STATA/Stata%20Programs)

---
# .brand-red[What can Rmarkdown do?]

.center[
<img src="assets/rmarkdown.jfif" height=500>
]

.font60[
Courtesy: Alison Horst [Artwork by @allison_horst](https://allisonhorst.com/) 
]

???

---
# .brand-red[For example: A reproducibility receipt]

.pull-left[
You can write something like this in Rmarkdown:

```r
sessioninfo::package_info() %>%
  unclass() %>%
  as_tibble() %>%
  filter(attached==TRUE) %>%
  select(package, ondiskversion, date) %>%
  rename(version=ondiskversion) %>%
  flextable() %>%
  autofit()
```

And it will come out like this in the document:
]

.pull-right[

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class="cl-6f5475e8">forcats</td><td class="cl-6f5475e9">0.5.2</td><td class="cl-6f5475ea">2022-08-19</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-6f5475eb">ggplot2</td><td class="cl-6f5475ec">3.4.0</td><td class="cl-6f549cf2">2022-11-04</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-6f549cf3">icons</td><td class="cl-6f549cf4">0.2.0</td><td class="cl-6f549cf5">2022-09-08</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-6f549cf6">patchwork</td><td class="cl-6f549cf7">1.1.2</td><td class="cl-6f549cf8">2022-08-19</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-6f549cf9">purrr</td><td class="cl-6f549cfa">0.3.5</td><td class="cl-6f549cfb">2022-10-06</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-6f549cf9">readr</td><td class="cl-6f549cfa">2.1.3</td><td class="cl-6f549cfb">2022-10-01</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-6f549cf3">readxl</td><td class="cl-6f549cf4">1.4.1</td><td class="cl-6f549cf5">2022-08-17</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-6f549cfc">RefManageR</td><td class="cl-6f54c40c">1.4.0</td><td class="cl-6f54c40d">2022-09-30</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-6f5475e8">sessioninfo</td><td class="cl-6f5475e9">1.2.2</td><td class="cl-6f5475ea">2021-12-06</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-6f5475e5">stringr</td><td class="cl-6f5475e6">1.4.1</td><td class="cl-6f5475e7">2022-08-20</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-6f549cf9">tibble</td><td class="cl-6f549cfa">3.1.8</td><td class="cl-6f549cfb">2022-07-22</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-6f5475e5">tidyr</td><td class="cl-6f5475e6">1.2.1</td><td class="cl-6f5475e7">2022-09-08</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-6f54c40e">tidyverse</td><td class="cl-6f54c40f">1.3.2</td><td class="cl-6f54c410">2022-07-18</td></tr></tbody></table></div></template>
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---

# .brand-red[What outputs can I create?]

.pull-left[

.content-box-yellow[

Documents

- PDF
- html
- **word**
- books

+more

Slides

- html
- powerpoint
- beamer

]
]

.pull-right[
 .content-box-red[

Other

- dashboards (flexdashboard)
- notebooks
- websites 
- shiny apps

]

[See here for examples](https://rmarkdown.rstudio.com/gallery.html)

]

???
today we are going to focus on word outputs, specifically using the officedown package
---

# .brand-red[Today we are focusing on:]
.pull-left[

.content-box-yellow[

- creating a word document
- basic formatting in markdown
- including code in report
- including tables in report
- including graphics in report
- cross reference tables and figures
- in line reporting

]
]

.pull-right[

.font60[
Courtesy: Alison Horst [Artwork by @allison_horst](https://allisonhorst.com/) 
]
]

???

- officedown package
- gtsummary package
- tidyverse approach to code
- tips and tricks along the way

---
class: sydney-blue

# **Some tips with Word + Rmarkdown:**

- knit regularly and check (esp figure size)

- use the code chunk option for table captions: 'tab.cap = "Insert table caption"'

- and code chunk option: 'tab.id="shortname"' with no symbols so you get "table 1"

- use global code chunk option "fig.cap = TRUE" to make sure Figure captions work

- "Clear knitr cache" is your friend, as is google and stackoverflow/github.

- if you are going to PDF it.... create a PDF document! .fn[1]

- if you want some cool features like interactive graphs & "sort-able" tables, try html!

.footnote[[1] Will need latex or tinytex installed! [Instructions here](https://bookdown.org/yihui/rmarkdown-cookbook/install-latex.html)]

---
# .brand-blue[**Resources:**]

.font130[**Rmarkdown**]

- [Rmarkdown cheatsheet](https://www.rstudio.org/links/r_markdown_cheat_sheet)
- [Rmarkdown reference](https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf)
- [Rmarkdown cookbook](https://bookdown.org/yihui/rmarkdown-cookbook/)

.font130[**gtsummary** @statistishdan]

- [gtsummary help with lots of examples](https://www.danieldsjoberg.com/gtsummary/)
- [gtsummary presentation](http://www.danieldsjoberg.com/gtsummary-weill-cornell-presentation/#1)
- super responsive on stackoverflow

.font130[**officedown** @DavidGohel]

- [Officedown for word](https://ardata-fr.github.io/officeverse/officedown-for-word.html)

???

---
class: sydney-red
background-image: url(assets/USydLogo-white.svg),url(https://upload.wikimedia.org/wikipedia/commons/b/be/Sharingan_triple.svg)
background-size: 260px,100px
background-position: 5% 95%,4% 70%

# Thanks!

.pull-right-2[
.pull-up[
 
]

.pull-down[

<a href="mailto:kristy.robledo@sydney.edu.au">
.white[<svg viewBox="0 0 512 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg"> <path d="M440 6.5L24 246.4c-34.4 19.9-31.1 70.8 5.7 85.9L144 379.6V464c0 46.4 59.2 65.5 86.6 28.6l43.8-59.1 111.9 46.2c5.9 2.4 12.1 3.6 18.3 3.6 8.2 0 16.3-2.1 23.6-6.2 12.8-7.2 21.6-20 23.9-34.5l59.4-387.2c6.1-40.1-36.9-68.8-71.5-48.9zM192 464v-64.6l36.6 15.1L192 464zm212.6-28.7l-153.8-63.5L391 169.5c10.7-15.5-9.5-33.5-23.7-21.2L155.8 332.6 48 288 464 48l-59.4 387.3z"></path></svg> kristy.robledo@sydney.edu.au]
</a>

<a href="https://kristyrobledo.github.io/Intro_Rmarkdown/">
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