second-section-new-chapter.qmd

# New Chapter

## Learning Objectives

Every chapter also needs Learning objectives.

## Libraries

For this chapter, we'll need the following packages attached:

*Remember to add [any additional packages you need to your course's own docker image](https://github.com/jhudsl/OTTR_Template/wiki/Using-Docker#starting-a-new-docker-image).

```{r}
library(magrittr)
```

## Topic of Section

You can write all your text in sections like this, using `##` to indicate a new header. you can use additional pound symbols to create lower levels of headers.

See [here](https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf) for additional general information about how you can format text within R Markdown files. In addition, see [here](https://pandoc.org/MANUAL.html#pandocs-markdown) for more in depth and advanced options.

### Subtopic

Here's a subheading (using three pound symbols) and some text in this subsection!

## Code examples

You can demonstrate code like this:

```{r}
output_dir <- file.path("resources", "code_output")
if (!dir.exists(output_dir)) {
  dir.create(output_dir)
}
```

And make plots too:

```{r}
hist_plot <- hist(iris$Sepal.Length)
```

You can also save these plots to file:

```{r}
png(file.path(output_dir, "test_plot.png"))
hist_plot
dev.off()
```


## Image example

How to include a Google slide. It's simplest to use the `ottrpal` package:

```{r}
#| fig-align: "center"
#| fig-alt: "Major point!! example image"
#| echo: false
#| out-width: "100%"
ottrpal::include_slide("https://docs.google.com/presentation/d/1Dw_rBb1hySN_76xh9-x5J2dWF_das9BAUjQigf2fN-E/edit#slide=id.g252f18e2576_1_0")
```

But if you have the slide or some other image locally downloaded you can also use HTML like this: 

<img src="resources/images/figure/1YmwKdIy9BeQ3EShgZhvtb3MgR8P6iDX4DfFD65W_gdQ_gcc4fbee202_0_141.png" title="Major point!! example image" alt="Major point!! example image" style="display: block; margin: auto; max-width: 100%; height: auto;" />


## Video examples

You may also want to embed videos in your course. If alternatively, you just want to include a link you can do so like this:

Check out this [link to a video](https://www.youtube.com/embed/VOCYL-FNbr0) using markdown syntax.

### Using `knitr`

To embed videos in your course, you can use `knitr::include_url()` like this:
Note that you should use `echo=FALSE` in the code chunk because we don't want the code part of this to show up. If you are unfamiliar with [how R Markdown code chunks work, read this](https://rmarkdown.rstudio.com/lesson-3.html).


```{r}
#| echo: false
knitr::include_url("https://www.youtube.com/embed/VOCYL-FNbr0")
```

### Using HTML

<iframe src="https://www.youtube.com/embed/VOCYL-FNbr0" width="672" height="400px"></iframe>

### Using `knitr`

```{r, fig.align="center", echo=FALSE, out.width="100%"}
knitr::include_url("https://drive.google.com/file/d/1mm72K4V7fqpgAfWkr6b7HTZrc3f-T6AV/preview")
```

### Using HTML

<iframe src="https://drive.google.com/file/d/1mm72K4V7fqpgAfWkr6b7HTZrc3f-T6AV/preview" width="672" height="800px"></iframe>

## Website Examples

Yet again you can use a link to a website like so:

[A Website](https://yihui.org)

You might want to have users open a website in a new tab by default, especially if they need to reference both the course and a resource at once.

[A Website](https://yihui.org){target="_blank"}

Or, you can embed some websites.

### Using `knitr`

This works:

```{r, fig.align="center", echo=FALSE}
knitr::include_url("https://yihui.org")
```


### Using HTML

<iframe src="https://yihui.org" width="672px" height="400px"></iframe>


## Stylized boxes

Occasionally, you might find it useful to emphasize a particular piece of information. To help you do so, we have provided css code and images (no need for you to worry about that!) to create the following stylized boxes.

You can use these boxes in your course with either of two options: using HTML code or Pandoc syntax.

### Using `rmarkdown` container syntax

The `rmarkdown` package allows for a different syntax to be converted to the HTML that you just saw and also allows for conversion to LaTeX. See the [Bookdown](https://bookdown.org/yihui/rmarkdown-cookbook/custom-blocks.html) documentation for more information. Note that Bookdown uses Pandoc.


```
::: {.notice}
Note using rmarkdown syntax.

:::
```

::: {.notice}
Note using rmarkdown syntax.

:::

As an example you might do something like this:

::: {.notice}
Please click on the subsection headers in the left hand
navigation bar (e.g., 2.1, 4.3) a second time to expand the
table of contents and enable the `scroll_highlight` feature
([see more](introduction.html#scroll-highlight))
:::


### Using HTML

To add a warning box like the following use:

<div class = "notice">
Followed by the text you want inside
</div>

This will create the following:

<div class = "notice">

Followed by the text you want inside

</div>

Here is a `<div class = "warning">` box:

<div class = "warning">

Note text

</div>

Here is a `<div class = "github">` box:

<div class = "github">

GitHub text

</div>


Here is a `<div class = "dictionary">` box:

<div class = "dictionary">

dictionary text

</div>


Here is a `<div class = "reflection">` box:

<div class = "reflection">

reflection text

</div>


Here is a `<div class = "wip">` box:

<div class = "wip">

Work in Progress text

</div>


## Dropdown summaries

<details><summary> You can hide additional information in a dropdown menu </summary>
Here's more words that are hidden.
</details>