02-chapter_of_course.Rmd

# A new chapter

*If you haven't yet read the getting started Wiki pages; [start there](https://github.com/jhudsl/OTTR_Template/wiki/Getting-started)

Every chapter needs to start out with this chunk of code:

```{r, include = FALSE}
ottrpal::set_knitr_image_path()
```

## Learning Objectives

*Every chapter also needs Learning objectives that will look like this:  

This chapter will cover:  

- {You can use https://tips.uark.edu/using-blooms-taxonomy/ to define some learning objectives here}
- {Another learning objective}

## 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)
```


## Subtopic

Here's a subheading 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', echo = FALSE, fig.alt= "Major point!! example image"}
ottrpal::include_slide("https://docs.google.com/presentation/d/1YmwKdIy9BeQ3EShgZhvtb3MgR8P6iDX4DfFD65W_gdQ/edit#slide=id.gcc4fbee202_0_141")
```

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

<img src="resources/images/02-chapter_of_course_files/figure-html//1YmwKdIy9BeQ3EShgZhvtb3MgR8P6iDX4DfFD65W_gdQ_gcc4fbee202_0_141.png" title="Major point!! example image" alt="Major point!! example image" style="display: block; margin: auto;" />

### Video examples

To show videos in your course, you can use markdown syntax like this:

[A video we want to show](https://www.youtube.com/embed/VOCYL-FNbr0)

Alternatively, you can use `knitr::include_url()` like this:
Note that we are using `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")
```

OR this works:

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

### Links to files

This works:

```{r, fig.align="center", echo=FALSE}
knitr::include_url("https://www.bgsu.edu/content/dam/BGSU/center-for-faculty-excellence/docs/TLGuides/TLGuide-Learning-Objectives.pdf", height = "800px")
```

Or this:

[This works](https://genetics-gsa.org/education/genetics-learning-framework/).

Or this:

<iframe src="https://genetics-gsa.org/education/genetics-learning-framework/" width="672" height="800px"></iframe>

### Links to websites

Examples of including a website link.

This works:

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

OR this:

![Another link](https://yihui.org)

OR this:

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

### Citation examples

We can put citations at the end of a sentence like this [@rmarkdown2021].
Or multiple citations [@rmarkdown2021, @Xie2018].

but they need a ; separator [@rmarkdown2021; @Xie2018].

In text, we can put citations like this @rmarkdown2021.

### Callout boxes

There are some preset callout boxes available, which can be used like so:

`notice`:

::: {.notice}
Here's something interesting.
:::

`warning`:

::: {.warning}
Look out!
:::

`dictionary`:

::: {.dictionary}
Here's a definition.
:::

`reflection`:

::: {.reflection}
Consider this!
:::

`github`:

::: {.github}
Here's how you use GitHub.
:::

`wip`:

::: {.wip}
This section is a **Work in Progress**.
:::

### Dropdown summaries

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

## Print out session info

You should print out session info when you have code for [reproducibility purposes](https://jhudatascience.org/Reproducibility_in_Cancer_Informatics/managing-package-versions.html).

```{r}
devtools::session_info()
```