<div class="bg-black white"  style="width:45%;right:0;bottom:0;padding-left:5px;border: solid 4px white;margin: auto;">
<i class="fas fa-exclamation-circle"></i> These slides are viewed best by Chrome and occasionally need to be refreshed if elements did not load properly. See here for <a href=session4.pdf>PDF <i class="fas fa-file-pdf"></i></a>. 
</div>

---

count: false
background-image: url(images/bg1.jpg)
background-size: cover
class: hide-slide-number title-slide

:::::::::: { .grid grid: 50% 50% / 1fr;} 
::: item center

# <span style="text-shadow: 2px 2px 30px white;">R Markdown Workshop</span>

<br><br>
## <span style="color:yellow;text-shadow: 2px 2px 30px black;">Reproducible Reports with R Markdown</span>

:::

::: center shade_black animated bounceInUp slower

Presented by Emi Tanaka

School of Mathematics and Statistics

<img src="assets/USydLogo-white.svg" style="width:200px"><br>
<span><i class="fas  fa-envelope faa-float animated "></i></span>  dr.emi.tanaka@gmail.com
<span><i class="fab  fa-twitter faa-float animated faa-fast "></i></span>  @statsgen

.bottom_abs.width100.bg-black[
1st Dec 2019 @ Biometrics by the Botanic Gardens | Adelaide, Australia
]

:::

::::::::::

---

---

# Cross Reference

::: grid

::: item

* When you make a header via Rmd
```markdown
# Some Header
```
 an .red[id is created automatically].
* The id is created by replacing .blue[space with `-`] and making it .blue[all lower case].
* Now you can link to this header by `[some text](#some-header)`.
* Cross references work for both pdf and html outputs.

:::

::: item

:::

---

# Direct Reference for `html`

<br>

::: paddings

* For `html` output, you can also give a link directly to the relevant section
* E.g. open `demo-header.html` in a web browser
* Append say `#chicken-data` to the url. It should look like 
.center[
`demo-header.html#chicken-data`
]
* It should have taken you to straight to the corresponding header 🏃

:::

---

# User-defined id

<br>

::: paddings

* You can define your own id by appending `{#your-id}`.

```markdown
# Some header {#header1}
```
* Now you can link to this header with the id `header1`.
* Note there should be no space in the id name!

:::

---

---

# Bibliography

* BibTeX citation style format is used to store references in `.bib` files.
* Remember that you can get most BibTeX citation for R packages `citation` function. (Scroll below to see the BibTeX citation).

```r
citation("xaringan")
```

```
  
  To cite package 'xaringan' in publications use:
  
    Yihui Xie (2019). xaringan: Presentation Ninja. R package version 0.9. https://CRAN.R-project.org/package=xaringan
  
  A BibTeX entry for LaTeX users is
  
    @Manual{,
      title = {xaringan: Presentation Ninja},
      author = {Yihui Xie},
      year = {2019},
      note = {R package version 0.9},
      url = {https://CRAN.R-project.org/package=xaringan},
    }
```
]

---

---

# Citations

<br>

::: paddings

* You can include BibTeX by specifying the `bib` file at YAML as:

```markdown
bibliography: bibliography.bib
```

[@bibtex-key] <i class="fas fa-arrow-right"></i> (Author et al. 2019)

@bibtex-key <i class="fas fa-arrow-right"></i> Author et al. 2019

* See `demo-citation.Rmd`

:::

---

# Figure References

::: paddings

* Support for figure references are included for output format type `bookdown::pdf_document2` for pdf or `bookdown::html_document2` for html.

````markdown
```{r plot1, fig.cap = "Caption"}
ggplot(cars, aes(dist, speed)) + geom_point()
```
````

* Above figure number can be referenced as .red[`\@ref(fig:plot1)`]

* The reference label has the prefix `fig:` before the chunk label.

:::

---

# Table References

::: paddings

* Support for table references are also included for output format type `bookdown::pdf_document2` for pdf or `bookdown::html_document2` for html.

````markdown
```{r table1}
knitr::kable(cars, booktabs = TRUE, caption = "Caption")
```
````

* Above table number can be referenced as .red[`\@ref(tab:table1)`]

* The reference label has the prefix `tab:` before the chunk label.

:::

---

# Markdown for Captions

::: paddings

````markdown
```{r plot1, fig.cap = "(ref:label)"}
ggplot(cars, aes(dist, speed)) + geom_point()
```
````

* Then the caption can be entered in a separate paragraph with empty lines above and below it

```markdown

(ref:label) This is the *caption* with **markdown**.

```

* You can substitute `label` with another unique label composed of alphanumeric characters, :, -, or /
* This caption supports markdown syntax
* This is great for long captions
* It also works for tables!

:::

---

---

# Parametrized Report

````markdown
---
title: "Parameterized Report"
params:
*  species: setosa 
output: html_document
---

```{r, message = FALSE, fig.dim = c(3,2)}
library(tidyverse)
iris %>% 
*  filter(Species==params$species) %>% 
   ggplot(aes(Sepal.Length, Sepal.Width)) +
   geom_point(aes(color=Species))
```
````

::: {.output .pos top:60px; right:10px;}
<img src = "images/parameterised-report-eg1.png" width = "550px"/>

:::

---

# Knit with Parameters

::: grid
::: item

```markdown
---
title: "Parameterized Report"
params:
  species: 
    label: "Species"
    value: setosa
    input: select
    choices: [setosa, versicolor, virginica]
  color: red
  max:
    label: "Maximum Sepal Width"
    value: 4
    input: slider
    min: 4
    max: 5
    step: 0.1
output: html_document
---
```

:::

::: item

````markdown
```{r, message = params$printmsg}
library(tidyverse)
iris %>% 
  filter(Species==params$species) %>% 
  filter(Sepal.Width < params$max) %>% 
  ggplot(aes(Sepal.Length, Sepal.Width)) +
  geom_point(color = params$color) + 
  labs(title = params$species)
```
````

:::

---

# Shiny Report Generator
::: grid
::: item 
```markdown
---
title: "Parameterized Report"
params:
  species: 
    label: "Species"
    value: setosa
    input: select
    choices: [setosa, versicolor, virginica]
  color: red
  max:
    label: "Maximum Sepal Width"
    value: 5
    input: slider
    min: 4
    max: 5
    step: 0.05
output: html_document
---
```

:::

::: item

<Br>

:::

---

---

# R Markdown via Command Line

::: grid

::: item

`demo-render.Rmd`

````markdown
---
title: "Parameterized Report"
params:
*  species: setosa
output: html_document
---

```{r, message = FALSE, fig.dim = c(3,2)}
library(tidyverse)
iris %>% 
*  filter(Species==params$species) %>% 
   ggplot(aes(Sepal.Length, Sepal.Width)) +
   geom_point(aes(color=Species))
```
````

:::

::: item

You can knit this file via R command by<br> using the `render` function:

```r
library(rmarkdown)
render("demo-render.Rmd")
```

<br>

You can overwrite the YAML values<br>  by supplying arguments to `render`:

```r
library(rmarkdown)
render("demo-render.Rmd", 
       output_format = "pdf_document",
       params = list(species = "virginica"))
```

:::

---

---

# Themes: `html_document`

<div id="myModal" class="modal">
  <div id="caption"></div>
  <span class="close" onclick="document.getElementById('myModal').style.display='none'">&times;</span>
  <iframe class="modal-content" id="img01"></iframe><br>
</div>

You can change the look of the html document by specifying themes:
::: grid

::: item

* `default` <img class="modalImg" alt="default"/> 
* `cerulean` <img class="modalImg" alt="cerulean"/> 
* `journal`  <img class="modalImg" alt="journal"/> 
* `flatly` <img class="modalImg" alt="flatly"/> 
* `darkly` <img class="modalImg" alt="darkly"/> 
* `readable` <img class="modalImg" alt="readable"/> 
* `spacelab` <img class="modalImg" alt="spacelab"/> 
* `united` <img class="modalImg" alt="united"/>

:::

::: item

* `cosmo` <img class="modalImg" alt="cosmo"/> 
* `lumen` <img class="modalImg" alt="lumen"/> 
* `paper` <img class="modalImg" alt="paper"/> 
* `sandstone` <img class="modalImg" alt="sandstone"/> 
* `simplex` <img class="modalImg" alt="simplex"/> 
* `yeti` <img class="modalImg" alt="yeti"/> 
* `NULL`  <img class="modalImg" alt="null"/>

:::

::: item

```markdown
output: 
  html_document:
    theme: cerulean
```

These [bootswatch](https://bootswatch.com/) themes attach the whole bootstrap library which makes your html file size larger.

:::

---

# `prettydoc`

<div id="myModal2" class="modal">
  <div id="caption2"></div>
  <span class="close" onclick="document.getElementById('myModal2').style.display='none'">&times;</span>
  <iframe class="modal-content" id="img02"></iframe><br>
</div>

::: grid

::: item

`prettydoc` 📦 is a community contributed `theme` that is light-weight:

* `cayman` <img class="modalImg2" alt="cayman"/> 
* `tactile` <img class="modalImg2" alt="tactile"/> 
* `architect` <img class="modalImg2" alt="architect"/> 
* `leonids` <img class="modalImg2" alt="leonids"/> 
* `hpstr` <img class="modalImg2" alt="hpstr"/>

:::

::: item

```markdown
output: 
  prettydoc::html_pretty:
    theme: cayman
```

See more about it below:

https://prettydoc.statr.me/

:::

---

# `rmdformats`

<div id="myModal3" class="modal">
  <div id="caption3"></div>
  <span class="close" onclick="document.getElementById('myModal3').style.display='none'">&times;</span>
  <iframe class="modal-content" id="img03"></iframe><br>
</div>

::: grid

::: item

`rmdformats` 📦 contains four built-in `html` formats:

* `readthedown` <img class="modalImg3" alt="readthedown"/> 
* `html_clean` <img class="modalImg3" alt="html_clean"/> 
* `html_docco` <img class="modalImg3" alt="html_docco"/> 
* `material` <img class="modalImg3" alt="material"/>

:::

::: item

You can use these formats by simply specifying the output in YAML as below:

```markdown
output: rmdformats::readthedown
```

See more about it below:

https://github.com/juba/rmdformats

:::

---

# `rticles` - LaTeX Journal Article Templates

<div id="myModal4" class="modal">
  <div id="caption4"></div>
  <span class="close" onclick="document.getElementById('myModal4').style.display='none'">&times;</span>
  <iframe class="modal-content" id="img04"></iframe><br>
</div>
::: grid
::: item 
* `acm` <img class='modalPdf' alt='acm_article'/>
* `acs` <img class='modalPdf' alt='acs_article'/>
* `aea` <img class='modalPdf' alt='aea_article'/>
* `agu` <img class='modalPdf' alt='agu_article'/>
* `amq` <img class='modalPdf' alt='amq_article'/>
* `ams` <img class='modalPdf' alt='ams_article'/>
* `asa` <img class='modalPdf' alt='asa_article'/>
* `biometrics` <img class='modalPdf' alt='biometrics_article'/>
* `copernicus` <img class='modalPdf' alt='copernicus_article'/>

:::

::: item

* `elsevier` <img class='modalPdf' alt='elsevier_article'/>
* `frontiers` <img class='modalPdf' alt='frontiers_article'/>
* `ieee` <img class='modalPdf' alt='ieee_article'/>
* `jss` <img class='modalPdf' alt='jss_article'/>
* `mdpi` <img class='modalPdf' alt='mdpi_article'/>
* `mnras` <img class='modalPdf' alt='mnras_article'/>
* `peerj` <img class='modalPdf' alt='peerj_article'/>
* `plos` <img class='modalPdf' alt='plos_article'/>

:::

::: item 
* `pnas` <img class='modalPdf' alt='pnas_article'/>
* `rjournal` <img class='modalPdf' alt='rjournal_article'/>
* `rsos` <img class='modalPdf' alt='rsos_article'/>
* `rss` <img class='modalPdf' alt='rss_article'/>
* `sage` <img class='modalPdf' alt='sage_article'/>
* `sim` <img class='modalPdf' alt='sim_article'/>
* `springer` <img class='modalPdf' alt='springer_article'/>
* `tf` <img class='modalPdf' alt='tf_article'/>

::::

::: {.bottom_abs .width100 .bg-indigo .white padding-left:10px;}
Go to RStudio > File > New File > R Markdown ... > From Template
:::

---

# External Files in Templating

::: grid

::: item

* When using `rticles`, each journal usually require external files (e.g. `cls` or image files).
* These external components are stored within the package.
* So use `draft` instead of `render`!

:::

::: item bg-gray

**GUI**

* `RStudio > File > New File > R Markdown ... > From Template`

**Command line**

```r
rmarkdown::draft("file.Rmd", 
 template = "biometrics_article",
 package = "rticles")
```

:::

---

# Making your own R Markdown template

::: paddings

* You need to make an R package first!<br>
Go to RStudio > New Project > New Directory > R Package or `usethis::create_package()`

* When you are in your R package project,

```r
usethis::use_rmarkdown_template("<Name>")
```

* Modify the `skeleton/skeleton.Rmd` to how you want and add all external files to the `skeleton` folder.
* Install your package.
* 🎉 And now find it at RStudio > File > New File > R Markdown > From Template.

:::

---

---

background-color: #e5e5e5

# Session Information

:::: scroll-350

```r
devtools::session_info()
```

```
  ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
   setting  value                       
   version  R version 3.6.0 (2019-04-26)
   os       macOS Mojave 10.14.6        
   system   x86_64, darwin15.6.0        
   ui       X11                         
   language (EN)                        
   collate  en_AU.UTF-8                 
   ctype    en_AU.UTF-8                 
   tz       Australia/Adelaide          
   date     2019-12-03                  
  
  ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
   package     * version    date       lib source                              
   anicon        0.1.0      2019-05-28 [1] Github (emitanaka/anicon@377aece)   
   assertthat    0.2.1      2019-03-21 [1] CRAN (R 3.6.0)                      
   backports     1.1.4      2019-04-10 [1] CRAN (R 3.6.0)                      
   broom         0.5.2      2019-04-07 [1] CRAN (R 3.6.0)                      
   callr         3.3.1      2019-07-18 [1] CRAN (R 3.6.0)                      
   cellranger    1.1.0      2016-07-27 [1] CRAN (R 3.6.0)                      
   cli           1.1.0      2019-03-19 [1] CRAN (R 3.6.0)                      
   colorspace    1.4-1      2019-03-18 [1] CRAN (R 3.6.0)                      
   countdown     0.2.0      2019-05-30 [1] Github (gadenbuie/countdown@c8e8710)
   crayon        1.3.4      2017-09-16 [1] CRAN (R 3.6.0)                      
   desc          1.2.0      2018-05-01 [1] CRAN (R 3.6.0)                      
   devtools      2.0.2      2019-04-08 [1] CRAN (R 3.6.0)                      
   digest        0.6.22     2019-10-21 [1] CRAN (R 3.6.0)                      
   dplyr       * 0.8.3      2019-07-04 [1] CRAN (R 3.6.0)                      
   emo           0.0.0.9000 2019-06-03 [1] Github (hadley/emo@02a5206)         
   evaluate      0.14       2019-05-28 [1] CRAN (R 3.6.0)                      
   forcats     * 0.4.0      2019-02-17 [1] CRAN (R 3.6.0)                      
   fs            1.3.1      2019-05-06 [1] CRAN (R 3.6.0)                      
   generics      0.0.2      2018-11-29 [1] CRAN (R 3.6.0)                      
   ggplot2     * 3.2.1      2019-08-10 [1] CRAN (R 3.6.0)                      
   glue          1.3.1.9000 2019-10-24 [1] Github (tidyverse/glue@71eeddf)     
   gtable        0.3.0      2019-03-25 [1] CRAN (R 3.6.0)                      
   haven         2.1.0      2019-02-19 [1] CRAN (R 3.6.0)                      
   hms           0.5.1      2019-08-23 [1] CRAN (R 3.6.0)                      
   htmltools     0.4.0      2019-10-04 [1] CRAN (R 3.6.0)                      
   httr          1.4.1      2019-08-05 [1] CRAN (R 3.6.0)                      
   icon          0.1.0      2019-05-28 [1] Github (ropenscilabs/icon@a510f88)  
   jsonlite      1.6        2018-12-07 [1] CRAN (R 3.6.0)                      
   knitr         1.25       2019-09-18 [1] CRAN (R 3.6.0)                      
   lattice       0.20-38    2018-11-04 [1] CRAN (R 3.6.0)                      
   lazyeval      0.2.2      2019-03-15 [1] CRAN (R 3.6.0)                      
   lifecycle     0.1.0      2019-08-01 [1] CRAN (R 3.6.0)                      
   lubridate     1.7.4      2018-04-11 [1] CRAN (R 3.6.0)                      
   magrittr      1.5        2014-11-22 [1] CRAN (R 3.6.0)                      
   memoise       1.1.0      2017-04-21 [1] CRAN (R 3.6.0)                      
   modelr        0.1.4      2019-02-18 [1] CRAN (R 3.6.0)                      
   munsell       0.5.0      2018-06-12 [1] CRAN (R 3.6.0)                      
   nlme          3.1-140    2019-05-12 [1] CRAN (R 3.6.0)                      
   pillar        1.4.2      2019-06-29 [1] CRAN (R 3.6.0)                      
   pkgbuild      1.0.3      2019-03-20 [1] CRAN (R 3.6.0)                      
   pkgconfig     2.0.3      2019-09-22 [1] CRAN (R 3.6.0)                      
   pkgload       1.0.2      2018-10-29 [1] CRAN (R 3.6.0)                      
   prettyunits   1.0.2      2015-07-13 [1] CRAN (R 3.6.0)                      
   processx      3.4.1      2019-07-18 [1] CRAN (R 3.6.0)                      
   ps            1.3.0      2018-12-21 [1] CRAN (R 3.6.0)                      
   purrr       * 0.3.2      2019-03-15 [1] CRAN (R 3.6.0)                      
   R6            2.4.0      2019-02-14 [1] CRAN (R 3.6.0)                      
   Rcpp          1.0.2      2019-07-25 [1] CRAN (R 3.6.0)                      
   readr       * 1.3.1      2018-12-21 [1] CRAN (R 3.6.0)                      
   readxl        1.3.1      2019-03-13 [1] CRAN (R 3.6.0)                      
   remotes       2.0.4      2019-04-10 [1] CRAN (R 3.6.0)                      
   rlang         0.4.0.9000 2019-08-03 [1] Github (r-lib/rlang@b0905db)        
   rmarkdown     1.16       2019-10-01 [1] CRAN (R 3.6.0)                      
   rprojroot     1.3-2      2018-01-03 [1] CRAN (R 3.6.0)                      
   rstudioapi    0.10       2019-03-19 [1] CRAN (R 3.6.0)                      
   rvest         0.3.4      2019-05-15 [1] CRAN (R 3.6.0)                      
   scales        1.0.0      2018-08-09 [1] CRAN (R 3.6.0)                      
   sessioninfo   1.1.1      2018-11-05 [1] CRAN (R 3.6.0)                      
   stringi       1.4.3      2019-03-12 [1] CRAN (R 3.6.0)                      
   stringr     * 1.4.0      2019-02-10 [1] CRAN (R 3.6.0)                      
   testthat      2.2.1      2019-07-25 [1] CRAN (R 3.6.0)                      
   tibble      * 2.1.3      2019-06-06 [1] CRAN (R 3.6.0)                      
   tidyr       * 1.0.0      2019-09-11 [1] CRAN (R 3.6.0)                      
   tidyselect    0.2.5      2018-10-11 [1] CRAN (R 3.6.0)                      
   tidyverse   * 1.2.1      2017-11-14 [1] CRAN (R 3.6.0)                      
   usethis       1.5.0      2019-04-07 [1] CRAN (R 3.6.0)                      
   vctrs         0.2.0.9000 2019-08-03 [1] Github (r-lib/vctrs@11c34ae)        
   whisker       0.3-2      2013-04-28 [1] CRAN (R 3.6.0)                      
   withr         2.1.2      2018-03-15 [1] CRAN (R 3.6.0)                      
   xaringan      0.9        2019-03-06 [1] CRAN (R 3.6.0)                      
   xfun          0.10       2019-10-01 [1] CRAN (R 3.6.0)                      
   xml2          1.2.0      2018-01-24 [1] CRAN (R 3.6.0)                      
   yaml          2.2.0      2018-07-25 [1] CRAN (R 3.6.0)                      
   zeallot       0.1.0      2018-01-28 [1] CRAN (R 3.6.0)                      
  
  [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library
```

<p></p>
:::

These slides are licensed under <br><center><a href="https://creativecommons.org/licenses/by-sa/3.0/au/"><img src="images/cc.svg" style="height:2em;"/><img src="images/by.svg" style="height:2em;"/><img src="images/sa.svg" style="height:2em;"/></a></center>

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1/27

R Markdown Workshop

Reproducible Reports with R Markdown

Presented by Emi Tanaka

School of Mathematics and Statistics

dr.emi.tanaka@gmail.com @statsgen

1st Dec 2019 @ Biometrics by the Botanic Gardens | Adelaide, Australia

1/27

🔎 Open and inspect the file

demo-header.Rmd

2/27

Cross ReferenceWhen you make a header via Rmd# Some Header

an id is created automatically.
The id is created by replacing space with - and making it all lower case.
Now you can link to this header by [some text](#some-header).
Cross references work for both pdf and html outputs.

3/27

Direct Reference for `html`

For html output, you can also give a link directly to the relevant section
E.g. open demo-header.html in a web browser
Append say #chicken-data to the url. It should look like
demo-header.html#chicken-data
It should have taken you to straight to the corresponding header 🏃

4/27

User-defined id

You can define your own id by appending {#your-id}.

# Some header {#header1}

Now you can link to this header with the id header1.
Note there should be no space in the id name!

5/27

🔍 Open and inspect the file

demo.bib

6/27

BibliographyBibTeX citation style format is used to store references in .bib files.
Remember that you can get most BibTeX citation for R packages citation function. (Scroll below to see the BibTeX citation).
citation("xaringan")

  To cite package 'xaringan' in publications use:
    Yihui Xie (2019). xaringan: Presentation Ninja. R package version 0.9. https://CRAN.R-project.org/package=xaringan
  A BibTeX entry for LaTeX users is
    @Manual{,
      title = {xaringan: Presentation Ninja},
      author = {Yihui Xie},
      year = {2019},
      note = {R package version 0.9},
      url = {https://CRAN.R-project.org/package=xaringan},
    }
7/27

🔍 Open, inspect and knit the file

demo-citation.Rmd

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Citations

You can include BibTeX by specifying the bib file at YAML as:

bibliography: bibliography.bib

[@bibtex-key] (Author et al. 2019)

@bibtex-key Author et al. 2019

See demo-citation.Rmd

9/27

Figure References

Support for figure references are included for output format type bookdown::pdf_document2 for pdf or bookdown::html_document2 for html.

```{r plot1, fig.cap = "Caption"}
ggplot(cars, aes(dist, speed)) + geom_point()
```

Above figure number can be referenced as \@ref(fig:plot1)
The reference label has the prefix fig: before the chunk label.

10/27

Table References

Support for table references are also included for output format type bookdown::pdf_document2 for pdf or bookdown::html_document2 for html.

```{r table1}
knitr::kable(cars, booktabs = TRUE, caption = "Caption")
```

Above table number can be referenced as \@ref(tab:table1)
The reference label has the prefix tab: before the chunk label.

11/27

Markdown for Captions```{r plot1, fig.cap = "(ref:label)"}
ggplot(cars, aes(dist, speed)) + geom_point()
```

Then the caption can be entered in a separate paragraph with empty lines above and below it

(ref:label) This is the *caption* with **markdown**.

You can substitute label with another unique label composed of alphanumeric characters, :, -, or /
This caption supports markdown syntax
This is great for long captions
It also works for tables!

12/27

🔧 Open and work through

challenge-12-references.Rmd

05:00

13/27

Parametrized Report

---
title: "Parameterized Report"
params:
   species: setosa 
output: html_document
---
```{r, message = FALSE, fig.dim = c(3,2)}
library(tidyverse)
iris %>% 
   filter(Species==params$species) %>% 
   ggplot(aes(Sepal.Length, Sepal.Width)) +
   geom_point(aes(color=Species))
```

14/27

Knit with Parameters

---
title: "Parameterized Report"
params:
  species: 
    label: "Species"
    value: setosa
    input: select
    choices: [setosa, versicolor, virginica]
  color: red
  max:
    label: "Maximum Sepal Width"
    value: 4
    input: slider
    min: 4
    max: 5
    step: 0.1
output: html_document
---

```{r, message = params$printmsg}
library(tidyverse)
iris %>% 
  filter(Species==params$species) %>% 
  filter(Sepal.Width < params$max) %>% 
  ggplot(aes(Sepal.Length, Sepal.Width)) +
  geom_point(color = params$color) + 
  labs(title = params$species)
```

15/27

Shiny Report Generator

---
title: "Parameterized Report"
params:
  species: 
    label: "Species"
    value: setosa
    input: select
    choices: [setosa, versicolor, virginica]
  color: red
  max:
    label: "Maximum Sepal Width"
    value: 5
    input: slider
    min: 4
    max: 5
    step: 0.05
output: html_document
---

16/27

🔧 Open and work through

challenge-13-params.Rmd

05:00

17/27

R Markdown via Command Line

demo-render.Rmd

---
title: "Parameterized Report"
params:
   species: setosa
output: html_document
---
```{r, message = FALSE, fig.dim = c(3,2)}
library(tidyverse)
iris %>% 
   filter(Species==params$species) %>% 
   ggplot(aes(Sepal.Length, Sepal.Width)) +
   geom_point(aes(color=Species))
```

You can knit this file via R command by
using the render function:

library(rmarkdown)
render("demo-render.Rmd")

You can overwrite the YAML values
by supplying arguments to render:

library(rmarkdown)
render("demo-render.Rmd", 
       output_format = "pdf_document",
       params = list(species = "virginica"))

18/27

🔧 Open and work through

challenge-14-letters.Rmd

10:00

19/27

Themes: `html_document`

You can change the look of the html document by specifying themes:

default
cerulean
journal
flatly
darkly
readable
spacelab
united

cosmo
lumen
paper
sandstone
simplex
yeti
NULL

output: 
  html_document:
    theme: cerulean

These bootswatch themes attach the whole bootstrap library which makes your html file size larger.

20/27

`prettydoc`

prettydoc 📦 is a community contributed theme that is light-weight:

cayman
tactile
architect
leonids
hpstr

output: 
  prettydoc::html_pretty:
    theme: cayman

See more about it below:

https://prettydoc.statr.me/

21/27

`rmdformats`

rmdformats 📦 contains four built-in html formats:

readthedown
html_clean
html_docco
material

You can use these formats by simply specifying the output in YAML as below:

output: rmdformats::readthedown

See more about it below:

https://github.com/juba/rmdformats

22/27

`rticles` - LaTeX Journal Article Templates

acm
acs
aea
agu
amq
ams
asa
biometrics
copernicus

elsevier
frontiers
ieee
jss
mdpi
mnras
peerj
plos

pnas
rjournal
rsos
rss
sage
sim
springer
tf

Go to RStudio > File > New File > R Markdown ... > From Template

23/27

External Files in Templating

When using rticles, each journal usually require external files (e.g. cls or image files).
These external components are stored within the package.
So use draft instead of render!

GUI

RStudio > File > New File > R Markdown ... > From Template

Command line

rmarkdown::draft("file.Rmd", 
 template = "biometrics_article",
 package = "rticles")

24/27

Making your own R Markdown templateYou need to make an R package first!

Go to RStudio > New Project > New Directory > R Package or usethis::create_package()

When you are in your R package project,

usethis::use_rmarkdown_template("<Name>")

Modify the skeleton/skeleton.Rmd to how you want and add all external files to the skeleton folder.
Install your package.
🎉 And now find it at RStudio > File > New File > R Markdown > From Template.

25/27

🔧 Create your own
R Markdown Template Package!

26/27

Session Information

devtools::session_info()

  ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
   setting  value                       
   version  R version 3.6.0 (2019-04-26)
   os       macOS Mojave 10.14.6        
   system   x86_64, darwin15.6.0        
   ui       X11                         
   language (EN)                        
   collate  en_AU.UTF-8                 
   ctype    en_AU.UTF-8                 
   tz       Australia/Adelaide          
   date     2019-12-03                  
  ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
   package     * version    date       lib source                              
   anicon        0.1.0      2019-05-28 [1] Github (emitanaka/anicon@377aece)   
   assertthat    0.2.1      2019-03-21 [1] CRAN (R 3.6.0)                      
   backports     1.1.4      2019-04-10 [1] CRAN (R 3.6.0)                      
   broom         0.5.2      2019-04-07 [1] CRAN (R 3.6.0)                      
   callr         3.3.1      2019-07-18 [1] CRAN (R 3.6.0)                      
   cellranger    1.1.0      2016-07-27 [1] CRAN (R 3.6.0)                      
   cli           1.1.0      2019-03-19 [1] CRAN (R 3.6.0)                      
   colorspace    1.4-1      2019-03-18 [1] CRAN (R 3.6.0)                      
   countdown     0.2.0      2019-05-30 [1] Github (gadenbuie/countdown@c8e8710)
   crayon        1.3.4      2017-09-16 [1] CRAN (R 3.6.0)                      
   desc          1.2.0      2018-05-01 [1] CRAN (R 3.6.0)                      
   devtools      2.0.2      2019-04-08 [1] CRAN (R 3.6.0)                      
   digest        0.6.22     2019-10-21 [1] CRAN (R 3.6.0)                      
   dplyr       * 0.8.3      2019-07-04 [1] CRAN (R 3.6.0)                      
   emo           0.0.0.9000 2019-06-03 [1] Github (hadley/emo@02a5206)         
   evaluate      0.14       2019-05-28 [1] CRAN (R 3.6.0)                      
   forcats     * 0.4.0      2019-02-17 [1] CRAN (R 3.6.0)                      
   fs            1.3.1      2019-05-06 [1] CRAN (R 3.6.0)                      
   generics      0.0.2      2018-11-29 [1] CRAN (R 3.6.0)                      
   ggplot2     * 3.2.1      2019-08-10 [1] CRAN (R 3.6.0)                      
   glue          1.3.1.9000 2019-10-24 [1] Github (tidyverse/glue@71eeddf)     
   gtable        0.3.0      2019-03-25 [1] CRAN (R 3.6.0)                      
   haven         2.1.0      2019-02-19 [1] CRAN (R 3.6.0)                      
   hms           0.5.1      2019-08-23 [1] CRAN (R 3.6.0)                      
   htmltools     0.4.0      2019-10-04 [1] CRAN (R 3.6.0)                      
   httr          1.4.1      2019-08-05 [1] CRAN (R 3.6.0)                      
   icon          0.1.0      2019-05-28 [1] Github (ropenscilabs/icon@a510f88)  
   jsonlite      1.6        2018-12-07 [1] CRAN (R 3.6.0)                      
   knitr         1.25       2019-09-18 [1] CRAN (R 3.6.0)                      
   lattice       0.20-38    2018-11-04 [1] CRAN (R 3.6.0)                      
   lazyeval      0.2.2      2019-03-15 [1] CRAN (R 3.6.0)                      
   lifecycle     0.1.0      2019-08-01 [1] CRAN (R 3.6.0)                      
   lubridate     1.7.4      2018-04-11 [1] CRAN (R 3.6.0)                      
   magrittr      1.5        2014-11-22 [1] CRAN (R 3.6.0)                      
   memoise       1.1.0      2017-04-21 [1] CRAN (R 3.6.0)                      
   modelr        0.1.4      2019-02-18 [1] CRAN (R 3.6.0)                      
   munsell       0.5.0      2018-06-12 [1] CRAN (R 3.6.0)                      
   nlme          3.1-140    2019-05-12 [1] CRAN (R 3.6.0)                      
   pillar        1.4.2      2019-06-29 [1] CRAN (R 3.6.0)                      
   pkgbuild      1.0.3      2019-03-20 [1] CRAN (R 3.6.0)                      
   pkgconfig     2.0.3      2019-09-22 [1] CRAN (R 3.6.0)                      
   pkgload       1.0.2      2018-10-29 [1] CRAN (R 3.6.0)                      
   prettyunits   1.0.2      2015-07-13 [1] CRAN (R 3.6.0)                      
   processx      3.4.1      2019-07-18 [1] CRAN (R 3.6.0)                      
   ps            1.3.0      2018-12-21 [1] CRAN (R 3.6.0)                      
   purrr       * 0.3.2      2019-03-15 [1] CRAN (R 3.6.0)                      
   R6            2.4.0      2019-02-14 [1] CRAN (R 3.6.0)                      
   Rcpp          1.0.2      2019-07-25 [1] CRAN (R 3.6.0)                      
   readr       * 1.3.1      2018-12-21 [1] CRAN (R 3.6.0)                      
   readxl        1.3.1      2019-03-13 [1] CRAN (R 3.6.0)                      
   remotes       2.0.4      2019-04-10 [1] CRAN (R 3.6.0)                      
   rlang         0.4.0.9000 2019-08-03 [1] Github (r-lib/rlang@b0905db)        
   rmarkdown     1.16       2019-10-01 [1] CRAN (R 3.6.0)                      
   rprojroot     1.3-2      2018-01-03 [1] CRAN (R 3.6.0)                      
   rstudioapi    0.10       2019-03-19 [1] CRAN (R 3.6.0)                      
   rvest         0.3.4      2019-05-15 [1] CRAN (R 3.6.0)                      
   scales        1.0.0      2018-08-09 [1] CRAN (R 3.6.0)                      
   sessioninfo   1.1.1      2018-11-05 [1] CRAN (R 3.6.0)                      
   stringi       1.4.3      2019-03-12 [1] CRAN (R 3.6.0)                      
   stringr     * 1.4.0      2019-02-10 [1] CRAN (R 3.6.0)                      
   testthat      2.2.1      2019-07-25 [1] CRAN (R 3.6.0)                      
   tibble      * 2.1.3      2019-06-06 [1] CRAN (R 3.6.0)                      
   tidyr       * 1.0.0      2019-09-11 [1] CRAN (R 3.6.0)                      
   tidyselect    0.2.5      2018-10-11 [1] CRAN (R 3.6.0)                      
   tidyverse   * 1.2.1      2017-11-14 [1] CRAN (R 3.6.0)                      
   usethis       1.5.0      2019-04-07 [1] CRAN (R 3.6.0)                      
   vctrs         0.2.0.9000 2019-08-03 [1] Github (r-lib/vctrs@11c34ae)        
   whisker       0.3-2      2013-04-28 [1] CRAN (R 3.6.0)                      
   withr         2.1.2      2018-03-15 [1] CRAN (R 3.6.0)                      
   xaringan      0.9        2019-03-06 [1] CRAN (R 3.6.0)                      
   xfun          0.10       2019-10-01 [1] CRAN (R 3.6.0)                      
   xml2          1.2.0      2018-01-24 [1] CRAN (R 3.6.0)                      
   yaml          2.2.0      2018-07-25 [1] CRAN (R 3.6.0)                      
   zeallot       0.1.0      2018-01-28 [1] CRAN (R 3.6.0)                      
  [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library

These slides are licensed under

27/27

R Markdown Workshop

Reproducible Reports with R Markdown

Presented by Emi Tanaka

School of Mathematics and Statistics

dr.emi.tanaka@gmail.com @statsgen

1st Dec 2019 @ Biometrics by the Botanic Gardens | Adelaide, Australia

1/27

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R Markdown Workshop

Reproducible Reports with R Markdown

Cross Reference

Direct Reference for html

User-defined id

Bibliography

Citations

Figure References

Table References

Markdown for Captions

Parametrized Report

Knit with Parameters

Shiny Report Generator

R Markdown via Command Line

Themes: html_document

prettydoc

rmdformats

rticles - LaTeX Journal Article Templates

External Files in Templating

Making your own R Markdown template

Session Information

R Markdown Workshop

Reproducible Reports with R Markdown

Help

Direct Reference for `html`

Themes: `html_document`

`prettydoc`

`rmdformats`

`rticles` - LaTeX Journal Article Templates