R Markdown Workshop

<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>

---

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# <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>
:::

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