tamu-slide-template.Rmd

---
title: "TAMU Presentation Template"
subtitle: "⚕<br/>with xaringan"
author: "Nan-Hung Hsieh"
date: ""
output:
  xaringan::moon_reader:
    css: ["default", "tamu.css", "tamu-fonts.css"]
    nature:
          highlightLines: true
---

class: inverse, center, middle
background-image: url(https://i.imgur.com/VCyLJx2.png)
background-size: contain

# Let's Get Started!

???

Image credit: [TAMU Brand Guide](https://brandguide.tamu.edu/images/brand-examples/ROI.jpg)

---

```{r setup, include=FALSE}
options(htmltools.dir.version = FALSE)
library(ggplot2)
library(MEMSS)
library(lattice)
```

class: inverse, center, middle
background-image: url(https://upload.wikimedia.org/wikipedia/commons/b/be/Sharingan_triple.svg)

???

Image credit: [Wikimedia Commons](https://commons.wikimedia.org/wiki/File:Sharingan_triple.svg)

---
class: inverse, center, middle

# xaringan

### /ʃæ.'riŋ.ɡæn/

---

# Hello **Ninja**

Xaringan is developed by Yihui Xie, the software engineer in [RStudio](https://www.rstudio.com).

You can install **xaringan** package from R CRAN or the latest version in [Github](https://github.com/yihui/xaringan)

```r
devtools::install_github("yihui/xaringan")
```

--

You are recommended to use the [RStudio IDE](https://www.rstudio.com/products/rstudio/), but you do not have to.

- Create a new R Markdown document from the menu `File -> New File -> R Markdown -> From Template -> Ninja Presentation`

--

- Click the `Knit` button to compile it;

--

- or use the [RStudio Addin](https://rstudio.github.io/rstudioaddins/)<sup>2</sup>; "Infinite Moon Reader" to live preview the slides (every time you update and save the Rmd document, the slides will be automatically reloaded in RStudio Viewer.

.footnote[
[1] See [#2](https://github.com/yihui/xaringan/issues/2) if you do not see the template or addin in RStudio.
]

---

# Why xaringan?

- **Free** and Open Source (Slides are composed in R Markdown)

- Version control

- Portable and easily share (Web-based slide)

- Easily print to PDF from Chrome

- [**Repoducibe**](Reproducibility) research result

.right[![Right-aligned image](http://phdcomics.com/comics/archive/phd031214s.gif)]

---
layout: true

background-image: url(https://brandguide.tamu.edu/downloads/logos/TAM-Logo.svg)
background-size: 100px
background-position: 99% 1% 

# TAMU theme

---

# 

The TAMU theme is based on [Texas A&M University University Brand Guide](https://brandguide.tamu.edu/). It consists of two CSS files.
To use this template (the latest version), go to [xaringan-tamu](https://github.com/nanhung/xaringan-tamu)
 github repo and clone it. You only need to put your slide file (`*.Rmd`) and the template css (`tamu.css`, `tamu-fonts.css`) in the same folder.

Then, use it in the YAML metadata, e.g.:

```yaml
---
title: "TAMU Presentation"
output:
  xaringan::moon_reader:
*    css: ["default", "tamu.css", "tamu-fonts.css"]
    nature:
          highlightLines: true
---
```
---

Not the GitHub User? **No Problem**!

Now, It's a built-in theme. Just simply revise the YAML:

```yaml
---
output:
  xaringan::moon_reader:
*    css: ["default", "tamu", "tamu-fonts"]
    nature:
          highlightLines: true
---
```
---
layout: false

# That's check some **functions**! 

A **FULL** image

![](https://brandguide.tamu.edu/assets/img/landing-page/ourbrand.jpg)

???
Image credit: [TAMU Brand Guide](https://brandguide.tamu.edu/assets/img/landing-page/ourbrand.jpg)

---

# **Look Good?**

<center><iframe src="https://giphy.com/embed/3ohzdP7FK3kyYgdWes" width="480" height="271" frameBorder="0" class="giphy-embed" allowFullScreen></iframe><p><a href="https://giphy.com/gifs/tamu-high-five-texas-am-3ohzdP7FK3kyYgdWes">via GIPHY</a></p></center>

---


# Foot note

Want to write the foot note? Embed the html script `<sup>1</sup>` like this<sup>1</sup>:

```r
.footnote[
[1] Y. Xie et al., xaringan: Presentation Ninja. 2018.
]
```

Also, this template was constructed refer to some examples<sup>2,3,4</sup>

.footnote[
[1] Y. Xie et al., xaringan: Presentation Ninja. 2018.  
[2] [R-Ladies presentation Ninja](https://alison.rbind.io/slides/rladies-demo-slides.html)  
[3] [Duke color template](https://www.johnlittle.info/project/custom/slide-template/duke_slide_template.html)  
[4] [Metropolis template](https://pat-s.github.io/files/xaringan-metropolis.html)  
]

---

# Font size

This is normal font size

Use `.large[]` to use .large[large font]

Use `.small[]` to use .small[small font]

<br/>

Also, you can try this trick

Use `.large[large[]]` to use .large[.large[**extra large font**]]

Use `.small[small[]]` to use .small[.small[**tiny font**]]

---

class: center

# Side by Side

.pull-left[

### TAM Logo Box

<img src="https://brandguide.tamu.edu/assets/downloads/logos/TAM-LogoBox.png" width="40%">

### TAM Logo

<img src="https://brandguide.tamu.edu/assets/downloads/logos/TAM-Logo.png" width="40%">
]

.pull-right[

### TAM Logo

<img src="https://brandguide.tamu.edu/assets/downloads/logos/TAM-Logo.png" width="40%">

### TAM Logo Box

<img src="https://brandguide.tamu.edu/assets/downloads/logos/TAM-LogoBox.png" width="40%">
]

---

# Image size

Use `.shrink[]` to shrink the image

.shrink[
![](https://brandguide.tamu.edu/assets/img/landing-page/ourbrand.jpg)
]

---

# Image size

Use `.enlarge[]` to enlarge the image

.enlarge[
![](https://brandguide.tamu.edu/assets/img/landing-page/ourbrand.jpg)
]


---


# Math Expressions

You can write LaTeX math expressions inside a pair of dollar signs. You can use the display style with double dollar signs. This is the [Hill equation](https://en.wikipedia.org/wiki/Hill_equation_(biochemistry):

```r
$$\theta=\frac{[L^n]}{k_d+[L]^n}$$
```

$$\theta=\frac{[L^n]}{k_d+[L]^n}$$

where  
- $\theta$ is the fraction of the receptor protein concentration that is bound to ligand.  
- $[L]$ is the free (unbound) ligand concentration.  
- $k_d$ is the apparent dissociation constant derived from the law of mass action (the equilibrium constant for dissociation). 

---

# R Code

```{r comment='#'}
# a boring regression
fit = lm(dist ~ 1 + speed, data = cars)
coef(summary(fit))
```


### Use the quote? No problem!
> "I came; I saw; I conquered"

```{r}
dojutsu = c('VENI', 'VIDI', 'VICI')
grep('VI', dojutsu, value = TRUE)
```

---

# R Plots

```{r, fig.height=3, dev='svg'}
ggplot(NULL, aes(x = 1, y = 1)) +
  annotate("text", 1, 1, label = 'GiG\'EM AGGIES!', color = "#500000",
           fontface = "bold", size = 12)+
  theme(axis.title = element_blank(), axis.ticks = element_blank(),
           axis.text = element_blank())
```

---

# Pharmacokinetics - Tables

If you want to generate a table, make sure it is in the HTML format (instead of Markdown or other formats), e.g.,

```{r}
knitr::kable(head(MEMSS::Theoph), format = 'html')
```

---

```{r eval=require('DT'), tidy=FALSE}
DT::datatable(
  head(MEMSS::Theoph, 120),
  fillContainer = FALSE, options = list(pageLength = 7)
)
```

---

# Pharmacokinetics - Plot

```{r, fig.height=4.5, dev='svg'}
xyplot(conc ~ Time| Subject, data=Theoph, xlab="Time (hr)",
       auto.key = T,
       ylab=expression(paste("Plasma concentration, ",mu, "M")), type="b")
```

---

# HTML Widgets - TAMU Map

```{r out.width='100%', fig.height=6, eval=require('leaflet')}
library(leaflet)
leaflet() %>% addTiles() %>% setView(lng = -96.3570, lat = 30.6116, zoom = 12)
```

---
# Highlight Lines

- The option `highlightLines: true` of `nature` will highlight code lines that start with `*`, or are wrapped in `{{ }}`, or have trailing comments `#<<`;

```yaml
output:
  xaringan::moon_reader:
    nature:
    highlightLines: true
```

.pull-left[
An example using `{{}}`:

    `r ''````{r tidy=FALSE}
    if (TRUE) {
    *{{ message("Very important!") }}
    }
    ```
]

.pull-right[

Output:
```{r tidy=FALSE}
if (TRUE) {
{{ message("Very important!") }}
}
```

]

---
class: middle

# Want to learn more functions? 
# [Click here!](https://slides.yihui.name/xaringan/incremental.html)

---
class: middle

# If you want to contribute a theme to **xaringan**, 
# please read [this blog post](https://yihui.name/en/2017/10/xaringan-themes). 

---
layout: false
class: inverse, center, middle

# **Thanks!**

Slides created via the R package [**xaringan**](https://github.com/yihui/xaringan).