---
execute: 
  echo: true
  message: false
  warning: false
format: 
  revealjs:
    highlight-style: a11y-dark
    reference-location: margin
    theme: lecture_styles.scss
    controls: true
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```{r}
#| echo = FALSE
require(downlit)
require(xml2)
```

## {#title-slide data-menu-title="Introduction to R, RStudio, and Quarto" background-image="../../images/csss-logo.png" background-position="center top 5%" background-size="50%" background="#1e4655"}

[Introduction to R, RStudio, and Quarto]{.custom-title}

[CS&SS 508 • Lecture 1]{.custom-subtitle}

[{{< var lectures.one >}}]{.custom-subtitle2}

[Victoria Sass]{.custom-subtitle3}


# Introductions & Syllabus{.section-title background-color="#99a486"}

## Welcome!

- Introductions
- Syllabus
- Lecture 1: Introduction to R, RStudio, and Quarto

## Who Am I? 

* Victoria (Vic) Sass

. . . 

* PhD Candidate in Sociology

. . . 

* I've been using `R` and `RStudio` for over 10 years 😱 

. . . 

* I love teaching this class 🤓

## Introductions

Let's start by getting to know each other a bit better. On your index card write the following: 

* Name and pronouns

* Program and year

* Experience with programming (in R or more generally)

* One word that best describes your feelings about taking this class

* Would you rather be able to converse with (non-human) animals, or have lifelong fluency in every (human) language?

. . . 

Pair up with someone nearby and introduce yourself to one another. Let's take about 5-10 minutes to do this. 


## Syllabus

The syllabus (as well as lots of other information) can be found on our course website:

<br>

**{{< var website.asis >}}**

<br>

Feel free to follow along online as I run through the syllabus!

## Course goals

This course is intended to give students a foundational understanding of programming in the statistical language R. This knowledge is intended to be broadly useful wherever you encounter data in your education and career. General topics we will focus on include:

:::{.incremental}
* Developing intermediate data management and visualization skills
* Organizing projects and creating reproducible research
* Cleaning data
* Linking multiple data sets together
* Learning basic programming skills
:::

. . . 

By the end of this course you should feel confident approaching any data you encounter in the future. We will cover almost no statistics, however it is the intention that this course will leave you prepared to progress in CS&SS or STAT courses with the ability to focus on statistics instead of coding. Additionally, the basic concepts you learn will be applicable to other programming languages and research in general, such as logic and algorithmic thinking.

## Logistics: General

**Lecture:** *On Tuesdays we will meet in the CSSCR lab for an interactive session where we'll cover a specific topic to help you learn fundamental skills, concepts, and principles for learning R. Additionally, these sessions will provide you with the opportunity to work with each other to learn and practice key skills in R. I will be available to answer questions and help troubleshoot code as well.*

**Office Hours:** *Drop-in to ask questions, get advice, or continue discussions from lab/lecture. We can talk in a breakout room or with the group!* 

  * Wednesdays, 11am-1pm (on Zoom; link on {{< var canvas >}})

::: {.callout-warning icon=false}

## <span style="color:orange">{{< fa comments >}}</span> **How to Contact Me**

Please {{< var message >}} in our {{< var slack.medium >}} rather than sending me an email. *I get far too many emails a day and I don't want to miss your message!* 

:::

## Logistics: Three Tools for Class

<br>

::: {.callout-tip icon=false}

## <span style="color:green">{{< fa brands slack >}}</span> Communication

Learning is collaborative! In addition to being the place to communicate with me, our **{{< var slack.short >}}** is also where you can ask one another questions, share resources, and just generally check in with each other about how your adventures with `R` are going. You can find the link to join our workplace on our course {{< var canvas >}}. 

:::

. . . 

::: {.callout-important icon=false}

## <span style="color:red">{{< fa upload >}}</span> Homework & Peer-Reviews

We will be using **{{< var canvas >}}** solely for homework & peer review submissions/deadlines and for any links I only want to distribute to those registered for this class (i.e. Slack and Office Hours Zoom).  

:::

. . . 

::: {.callout-note icon=false}

## <span style="color:blue">{{< fa laptop-code >}}</span> Course Content

All course content will be accessible on our course website: **{{< var website.asis >}}**.

:::

## <span style="color:#99a486">{{< fa brands slack >}}</span> Slack 

If you've never used Slack before you'll need to [download the desktop app](https://www.slack.com/download?_gl=1*l0hwaq*_gcl_au*MTM3NjIzOTUyMy4xNjk1Njg3MTg5*_ga*MzIxNjQyMzI3LjE2OTU2ODcxOTA.*_ga_QTJQME5M5D*MTY5NjE2Mjc4Ny41LjAuMTY5NjE2Mjc4Ny42MC4wLjA.). 

. . . 

A useful quick-start guide can be found [here](https://slack.com/help/articles/360059928654-How-to-use-Slack--your-quick-start-guide). 

. . . 

Go to our {{< var canvas >}} site for the invite link to join our private workspace. 

## Schedule

. . . 

:::: {.columns}
::: {.column width="20%"}
March 26\
\
April 2\
\
April 9\
\
April 16\
\
April 23\
\
April 30\
\
May 7\
\
May 14\
\
May 21\
\
May 28\

:::
::: {.column width="10%"}
<span style="color:#4e79a7">{{< fa r >}}</span> \
\
<span style="color:#f28e2c">{{< fa chart-line >}}</span> \
\
<span style="color:#e15759">{{< fa diagram-next >}}</span> \
\
<span style="color:#76b7b2">{{< fa broom >}}</span> \
\
<span style="color:#59a14f">{{< fa table >}}</span> \
\
<span style="color:#edc949">{{< fa cubes >}}</span> \
\
<span style="color:#af7aa1">{{< fa comments >}}</span> \
\
<span style="color:#ff9da7">{{< fa florin-sign >}}</span> \
\
<span style="color:#9c755f">{{< fa arrows-spin >}}</span> \
\
<span style="color:#bab0ab">{{< fa forward >}}</span> \
:::
::: {.column width="70%"}
Week 1: Introduction to R, RStudio, and Quarto\
\
Week 2: Visualizing Data\
\
Week 3: Workflow and Reproducibility\
\
Week 4: Importing, Exporting, and Cleaning Data\
\
Week 5: Manipulating and Summarizing Data\
\
Week 6: Data Structures & Types\
\
Week 7: Working with Text Data\
\
Week 8: Writing Functions\
\
Week 9: Iteration\
\
Week 10: Next Steps\
:::
::::

## Prerequisites 

. . . 

::: {.r-fit-text}
<span style="color:#1e4655">None 😎</span> 
:::

## Course Materials

**Materials:** All course materials will be provided on the {{< var website.linked >}}. This includes:

* Lecture slides and the code used to generate them.
* Homework instructions and/or templates.
* Recommended reading/cheatsheet(s).
* Useful links to other resources.

**Laptops:** You're welcome to bring a laptop to class if you'd prefer to use your own machine.

::: {.callout-note icon=false}

## <span style="color:blue">{{< fa circle-info >}}</span> \ Keep In Mind
The versions of `R`, RStudio, and Quarto (as well as any packages you have installed) will not necessarily be the same/up to date if you do your work on different computers. My advice is to consistently use the same device for homework assignments or to make sure to download the latest versions of `R`, RStudio, and Quarto when using a new machine. 
:::

## Readings

:::: {.columns}

::: {.column width="50%"}

<br>

**Textbooks:** This course has no textbook. However, I will be suggesting selections from [R for Data Science](https://r4ds.hadley.nz/) to pair with each week's topic. While not required, I strongly suggest reading those selections before doing the homework for that week. 
:::

::: {.column width="50%"}

![](images/r4dsv2.jpeg){width=90%}
:::


::::



## Course Assessment 

### Final grade
Credit/No Credit (C/NC); You need at least 60% to get Credit

:::: {.columns}
::: {.column width="50%"}
#### Homework (75%; assessed by peers)
9 total homeworks; assessed on a 0-3 point rubric. Assigned at the end of lecture sessions and due a week later.
```{r}
#| echo: false
#| warning: false
#| message: false

source("../../Homework/rubric.R")

rubric |> 
  tab_options(table.align = "center", table.font.size = pct(70))
  
```
:::
::: {.column width="50%"}
#### Peer Grading (25%; assessed by me)
One per homework, assessed on a binary *satisfactory*/*unsatisfactory* scale. Due 5 days after homework due date. 

```{r}
#| echo: false
#| warning: false
#| message: false
peer_review_rubric |> 
  tab_options(table.align = "center", table.font.size = pct(70))
```
:::
::::

## Due Dates and Late Policy 

Homework/peer grading instructions and deadlines can be found on the [Homework](https://vsass.github.io/CSSS508/Homework/homework.html) page of the course website. All homework will be turned in on {{< var canvas >}} **by 4:30pm the day it is due**.

::: {.callout-important icon=false}
## <span style="color:red">{{< fa triangle-exclamation >}}</span> Late Homework Will Automatically Lose Peer-Review Credit

Peer reviews are randomly assigned when the due date/time is reached. Therefore, if you don't submit your homework on time, you will not be given a peer's homework to review and vice versa. That said, life is messy and complicated and we all miss deadlines for a variety of reasons. Therefore, you can request that I review and provide feedback on a late assignment ({{< var message >}} on Slack) but you won't be able to earn peer-review credit for that particular homework. 
:::

## Ugh, peer grading?

Yes, because:

* You will write your reports better knowing others will see them

* You learn alternate approaches to the same problem

* You will have more opportunities to practice and have the material sink in

. . . 

How to peer review:

* Leave **constructive comments**: You'll only get the point if you write at least several sentences that includes
    + Any key issues from the assignment and,
    + Points out something positive in your peer's work.
* **Send me a message on Slack** if you would like your assignment to be regraded or for me to provide feedback if no peer review was given.

## Academic Integrity

Academic integrity is essential to this course and to your learning. Violations of the academic integrity policy include but are not limited to: 

* Copying from a peer
* Copying from an online resource
* Using resources from a previous iteration of the course. 

. . . 

I hope you will collaborate with peers on assignments and use Internet resources when questions arise to help solve issues. The key is that you **ultimately submit your own work**. 

. . . 

Anything found in violation of this policy will be automatically given a score of 0 with no exceptions. If the situation merits, it will also be reported to the UW Student Conduct Office, at which point it is out of my hands. If you have any questions about this policy, please do not hesitate to reach out and ask.

## Classroom Environment

I'm committed to fostering a friendly and inclusive classroom environment in which all students have an equal opportunity to learn and succeed. This course is an attempt to make an often difficult and frustrating experience (learning `R` for the first time) less obfuscating, daunting, and stressful. That said, learning happens in different ways at at a different pace for everyone. Learning is *also* a collaborative and creative process and my aim is to create an environment in which you all feel comfortable asking questions of me *and* each other. Treat **your peers** and **yourself** with empathy and respect as you all approach this topic from a range of backgrounds and experiences (in programming and in life). 

## Classroom Environment...

**Names & Pronouns:** Everyone deserves to be addressed respectfully and correctly. Fill out your profile on Slack with your picture, preferred name (as your Display Name), and correct gender pronouns so we can all be on the same page!

. . . 

**Covid Considerations:** I will follow all University rules and procedures regarding Covid, which may or may not change during the quarter. I also recognize that Covid creates unique circumstances and concerns for each of us, which may limit your ability to fully attend or participate in this course. You never need to apologize to me for anything pandemic-related. If there is something I can do to make you feel more comfortable during class, please let me know!

. . . 

**Diversity:** Diverse backgrounds, embodiments, and experiences are essential to the critical thinking endeavor at the heart of university education. Therefore, I expect you to follow the [UW Student Conduct Code](https://www.washington.edu/cssc/for-students/student-code-of-conduct/) in your interactions with your colleagues and me in this course by respecting the many social and cultural differences among us, which may include, but are not limited to: age, cultural background, disability, ethnicity, family status, gender identity and presentation, body size/shape, citizenship and immigration status, national origin, race, religious and political beliefs, sex, sexual orientation, socioeconomic status, and veteran status.

## Accommodations

**Accessibility & Accommodations:** Your experience in this class is important to me. If you have already established accommodations with Disability Resources for Students (DRS), please communicate your approved accommodations to me at your earliest convenience so we can discuss your needs in this course. If you have not yet established services through DRS, but have a temporary health condition or permanent disability that requires accommodations (conditions include but not limited to; mental health, attention-related, learning, vision, hearing, physical or health impacts), you are welcome to contact DRS at 206-543-8924, [uwdrs\@uw.edu](mailto:uwdrs@uw.edu), or through their [website](https://depts.washington.edu/uwdrs/).

. . . 

**Religious Accommodations:** Washington state law requires that UW develop a policy for accommodation of student absences or significant hardship due to reasons of faith or conscience, or for organized religious activities. The UW\'s policy, including more information about how to request an accommodation, is available at [Religious Accommodations Policy](https://registrar.washington.edu/staffandfaculty/religious-accommodations-policy/). Accommodations must be requested within the first two weeks of this course using the [Religious Accommodations Request form](https://registrar.washington.edu/students/religious-accommodations-request/).

## Help and Feedback

**Getting Help:** If at any point during the quarter you find yourself struggling to keep up, please let me know! I am here to help. A great place to start this process is by chatting before^[Unfortunately I have to leave right after class to catch the ferry so if you want to chat in person, come early to class. I'll be hanging out starting at 4pm each Tuesday.] class, coming to office hours, or {{< var message >}}on Slack. 

. . . 

Also, help one another as you navigate this course! Slack allows you to chat directly with one another, send messages to the whole class about specific topics (see the already-created **# r-code-questions** and **# quarto-questions** channels), send snippets of code or entire files to one another, and much more. 

. . . 

::: {.callout-tip icon=false}
## <span style="color:green">{{< fa message >}}</span> Feedback
If you have feedback on any part of this course or the classroom environment I want to hear it! You can {{< var message >}} directly on Slack or send me an anonymous message [here](https://web.polly.ai/fgajfc). Additionally, I will send out a mid-quarter feedback survey on Slack around Week 5.
:::

## Asking Questions

Don't ask like this:

> tried lm(y~x) but it iddn't work wat do

. . . 

Instead, ask like this: 

<blockquote>
```
y <- seq(1:10) + rnorm(10)
x <- seq(0:10)
model <- lm(y ~ x)
```

Running the block above gives me the following error, anyone know why?

```
Error in model.frame.default(formula = y ~ x, 
drop.unused.levels = TRUE) : variable lengths differ 
(found for 'x')
```
</blockquote>

::: {.callout-caution icon=false}
## <span style="color:tomato">{{< fa share-from-square >}}</span> FYI
If you ask me a question directly over Slack I may send out your question (anonymously) along with my answer to the whole course.
:::

                         

# Questions?{.section-title background-color="#99a486"}

# Introduction to R, RStudio, and Quarto{.section-title background-color="#99a486"}

## A Note on Slide Formatting {auto-animate="true"}

**Bold** usually indicates an important vocabulary term. Remember these!

. . . 

*Italics* indicate emphasis but also are used to point out things you must click with a mouse. 
  
   * For example: "Please click *File* > *Print*"

. . . 

`Code` represents R code you could use to perform actions. 

   * For example: "Press `Ctrl-P` to open the print dialogue."

. . . 

Code chunks that span the page represent *actual R code embedded in the slides*.

```{r}
#| eval: false
7 * 49
```

## A Note on Slide Formatting {auto-animate="true"}

**Bold** usually indicates an important vocabulary term. Remember these!

*Italics* indicate emphasis but also are used to point out things you must click with a mouse. 
  
   * For example: "Please click *File* > *Print*"

`Code` represents R code you could use to perform actions. 

   * For example: "Press `Ctrl-P` to open the print dialogue."

Code chunks that span the page represent *actual R code embedded in the slides*.

```{r}
#| eval: false
#| code-line-numbers: "2"
7 * 49 
# Sometimes important stuff is highlighted!
```

## A Note on How to Use These Slides <span style="color:#99a486">{{< fa scroll >}}</span> {.scrollable} 

Since the lectures for this class were created using Quarto, there are numerous built-in features meant to facilitate your learning, particularly of `R`.

::: {.incremental}
1. The <span style="color:#1e4655">{{< fa bars >}}</span> in the bottom left-hand corner will show you a table of contents for the entire slideshow, allowing you to find what you're looking for more easily. 
2. Anything followed by <span style="color:#1e4655">{{< fa arrow-up-right-from-square >}}</span> is a link to an external site. You will be shown a preview (if available) within the presentation first and from there you can open the link in a new tab to explore it more. 
3. If you hover over any chunk of `R` code embedded in the slides you will see a <span style="color:#1e4655">{{< fa clipboard >}}</span> which you can click to copy the code. You can then paste it in your own Quarto document or `R` script to run it in your session of RStudio. 
4. To get a PDF version of these slides click *File* > *Print* from your internet browser, select *Save as PDF* as the Destination or Printer, and make sure the Layout is set to *Landscape*. (Note: the *PDF Export Mode* in *Tools* actually cuts off content which is why I'm not recommending it)
5. Clicking on the <span style="color:#1e4655">{{< fa paintbrush >}}</span> in the bottom left-hand corner allows you to draw directly on the slides, in a very Microsoft Paint kind of way. See if it's useful but I make no promises!
6. Type **?** at any time to see all the available key-board shortcuts. 
7. Some content may be scrollable (like this page!). If this is the case I will put the <span style="color:#99a486">{{< fa scroll >}}</span> icon in the title to let you know. 
:::


## Why R?

R is a programming language built for statistical computing.

If one already knows Stata or similar software, why use R?

. . . 

* R is *free*.

. . . 

* R has a *very* large community.

. . . 

* R can handle virtually any data format.

. . . 

* R makes replication easy.

. . . 

* R is a *language* so it can do *everything*.

. . . 

* R skills transfer to other languages like Python and Julia.

## R Studio

R Studio is a "front-end" or integrated development environment (IDE) for R that can make your life *easier*.

. . . 

We'll show RStudio can...

::: {.incremental}
* Organize your code, output, and plots
* Auto-complete code and highlight syntax
* Help view data and objects
* Enable easy integration of R code into documents with **Quarto**
:::

. . . 

It can also...

* Manage `git` repositories

* Run interactive tutorials

* Handle other languages like C++, Python, SQL, HTML, and shell scripting

## Selling You on Quarto

Built upon many of the developments of the R Markdown ecosystem, Quarto distills them into one coherent system and additionally expands its functionality by supporting other programming languages besides R, including Python and Julia. 

![](images/rmarkdown-quarto.png){fig-align="center"}

## Selling You on Quarto

The ability to create Quarto files in R is a powerful advantage. It allows us to:

:::{.incremental}
* Document analyses by combining text, code, and output
   + No copying and pasting into Word
   + Easy for collaborators to understand
   + Show as little or as much code as you want
* Produce many different document types as output
  + PDF documents
  + HTML webpages and reports
  + Word and PowerPoint documents  
  + Presentations (like these slides)
  + Books
  + Theses/Dissertations 😉🎓
  + Websites (like the one for [this course](http://vsass.github.io/CSSS508)!)
* Works with LaTeX and HTML for math and more formatting control
:::

## Downloading R and RStudio 

If you don't already have R and RStudio on your machine, now is the time to do so!

:::{.incremental}
1. Go to the course homepage, <https://vsass.github.io/CSSS508>
2. Click the *Download R* link and download R to your machine.
3. Afterwards, click the *Download RStudio* link and download RStudio to your machine.
4. Lastly, click the *Download Quarto* link and download Quarto to your machine. 
:::

## Getting Started

Open up RStudio now and choose *File > New File > R Script*.

Then, let's get oriented with the interface:

:::{.incremental}
* *Top Left*: Code **editor** pane, data viewer (browse with tabs)

* *Bottom Left*: **Console** for running code (`>` prompt)

* *Top Right*: List of objects in **environment**, code **history** tab.

* *Bottom Right*: Tabs for browsing files, viewing plots, managing packages, and viewing help files.
:::

## {data-menu-title="RStudio IDE image" background-image="images/rstudio-panes-labeled.jpeg" background-size=70%}

## Editing and Running Code

There are several ways to run R code in RStudio:

. . . 

* Highlight lines in the **editor** window and click <span>&emsp;&emsp;&ensp;</span> ![](images/rtudio_run.png){.absolute top=105 right=430} *Run* at the top right corner of said window or hit `Ctrl+Enter` or `⌘+Enter` to run them all.

## Editing and Running Code

There are several ways to run R code in RStudio:

* Highlight lines in the **editor** window and click <span>&emsp;&emsp;&ensp;</span> ![](images/rtudio_run.png){.absolute top=105 right=430} *Run* at the top right corner of said window or hit `Ctrl+Enter` or `⌘+Enter` to run them all.

* With your **caret**^[This thing is the caret: <span class="blink_me">|</span>] on a line you want to run, hit `Ctrl+Enter` or `⌘+Enter`. Note your caret moves to the next line, so you can run code sequentially with repeated presses.

. . . 

* Type individual lines in the **console** and press `Enter`.

. . . 

* In quarto documents, click within a code chunk and click the green arrow <span>&emsp;&nbsp;</span> ![](images/rstudio_run_current_chunk.png){.absolute top=355 right=135} to run the chunk. The button beside that (<span>&emsp;&emsp;</span> ![](images/rstudio_run_all_chunks_above.png){.absolute top=392 right=615}) runs *all prior chunks*.

. . .

The console will show the lines you ran followed by any printed output.

## Incomplete Code

If you mess up (e.g. leave off a parenthesis), R might show a `+` sign prompting you to finish the command:

```{r Coding 1}
#| eval: false
> (11-2
+
```

Finish the command or hit `Esc` to get out of this.

## R as a Calculator

In the **console**, type `123 + 456 + 789` and hit `Enter`.

. . . 

```{r Calc 1}
123 + 456 + 789
```

. . . 

The `[1]` in the output indicates the numeric **index** of the first element on that line.

. . . 

Now in your blank R document in the **editor**, try typing the line `sqrt(400)` and either
clicking *Run* or hitting `Ctrl+Enter` or `⌘+Enter`.

. . . 

```{r Calc 2}
#| echo: true
sqrt(400)
```

## Functions

`sqrt()` is an example of a **function** in R.



**Arguments** are the *inputs* to a function. In this case, the only argument to `sqrt()`
is `x` which can be a number or a vector of numbers.

<br>

. . . 

The basic template of a function is

`function_name(argument1, argument2 = value2, argument3 = value3...)`

<br> 

. . . 

::: {.callout-note icon=false}

## <span style="color:blue">{{< fa circle-info >}}</span> \ Something to Note
Functions can have a wide range of arguments and some are *required* for the function to run, while others remain optional. You can see from each functions' help page which are not required because they will have an `=` with some default value pre-selected. If there is no `=` it is up to the user to define that value and it's therefore a required specification.
:::

## Help

:::: {.columns}
::: {.column width="50%"}

If we didn't have a good guess as to what `sqrt()` will do, we can type `?sqrt` in the console and look at the **Help** panel on the bottom right.

```{r Help}
#| eval: false
?sqrt
```

<br>

If you're trying to look up the help page for a function and can't remember its name you can search by a keyword and you will get a list of help pages containing said keyword. 

```{r Search help}
#| eval: false
??exponential
```

:::
::: {.column width="50%"}

![](images/help_page.png)
:::
::::

## Help

Help files provide documentation on how to use functions and what functions produce. They will generally consist of the following sections:

* **Description** - *What does it do?*
* **Usage** - *How do you write it?*
* **Arguments** - *What arguments does it take; which are required; what are the defaults?*
* **Details** - *A more in-depth description* 
* **Value** - *What does the function return?*
* **See Also** - *Related R functions*
* **Examples** - *Example (& reproducible) code*

## Objects

R stores everything as an **object**, including data, functions, models, and output.

. . . 

Creating an object can be done using the **assignment operator**: `<-` 
. . . 

```{r Objects 1}
new.object <- 144
```

. . . 

**Operators** like `<-` are functions that look like symbols but typically sit between their arguments 
(e.g. numbers or objects) instead of having them inside `()` like in `sqrt(x)`. 

. . . 

We do math with operators, e.g., `x + y`. 

`+` is the addition operator!

## Calling Objects

You can display or "call" an object simply by using its name.

```{r Objects 2}
new.object
```

## Naming Objects

Object names must begin with a letter and can contain letters, numbers, `.`, and `_`.

Try to be consistent in naming objects. RStudio auto-complete means **long, descriptive names are better than short, vague ones**! *Good names save confusion later!*

. . . 

* *snake_case*, where you separate lowercase words with `_` is a common and practical naming convention that I strongly recommend.

```{r}
#| eval: false
snake_case_is_easy_to_read
CamelCaseIsAlsoAnOptionButSortOfHardToReadQuickly
some.people.use.periods
And_some.People_ARETRUErebels
```

. . . 

<br>

Remember that object names are **CaSe SeNsItIvE!!** 

Also, **TYPOS MATTER**! 


## Using Objects

An object's **name** represents the information stored in that **object**, so you can treat the object's name as if it were the values stored inside.
. . . 

```{r Objects 3}
new.object + 10
new.object + new.object
sqrt(new.object)
```

## Comments 

Anything writen after `#`^[In Quarto documents, comments only work in code chunks. Outside of a chunk, `#` creates **headers** like "comments" at the top of this slide.] will be ignorned by R. 

```{r}
# create vector of ages of students
ages <- c(45, 21, 27, 34, 23, 24, 24)

# get average age of students
mean(ages)
```

. . . 

Comments help collaborators and future-you understand *what*, and more importantly, **why** you are doing what you're doing with that specific line/chunk of code. 

. . . 

Additionally, comments allow you to explain your overall coding plan and record anything important that you've discovered along the way. 

## Vectors

A **vector** is one of many data types available in `R`. Specifically, it is a series of **elements**, such as numbers, strings, or booleans (i.e. `TRUE`, `FALSE`).

. . . 

You can create a vector using the function `c()` which stands for "**c**ombine" or "**c**oncatenate".
. . . 

```{r Vectors 1}
new.object <- c(4, 9, 16, 25, 36)
new.object
```

. . . 

If you name an object the same name as an existing object, *it will overwrite it*.

. . . 

You can provide a vector as an argument for many functions.
. . . 

```{r Vectors 2}
sqrt(new.object)
```

## More Complex Objects

There are other, more complex data types in R which we will discuss later in the quarter! These include **matrices**, **arrays**, **lists**, and **dataframes**.

Most data sets you will work with will be read into `R` and stored as a **dataframe**, so this course will mainly focus on manipulating and visualizing these objects.

# Quarto{.section-title background-color="#99a486"}

## Creating a Quarto Document

Let's try making an Quarto file:

1. Choose *File > New File > Quarto Document...*
2. Make sure *HTML Output* is selected 
3. In the *Title* box call this test document `My First Qmd` and click *Create*
4. Save this document somewhere (you can delete it later) (either with *File > Save* or clicking <span>&emsp;&ensp;</span> ![](images/rstudio_save.png){.absolute top=284 left=23} towards the top left of the source pane).
5. Lastly, click <span>&emsp;&emsp;</span> ![](images/rstudio_render.png){.absolute top=320 left=157} Render at the top of the source pan to "knit" your document into an html file. This will produce a minimal webpage since we only have a title. We need to add more content!

. . . 

If you want to create PDF output in the future, you'll need to run the following code in your console. 

```{r PDFHelp}
#| eval: false
install.packages("quarto")
install.packages('tinytex')
tinytex::install_tinytex()
```

## Anatomy of a Quarto Document

:::: {.columns}

::: {.column width="50%"}


::: {.panel-tabset}

### Quarto file

```{r}
#| echo: false
#| comment: ""
   
cat(readr::read_file("quarto_anatomy.qmd"))
```

### Rendered html document

```{r}
#| label: quarto-anatomy
#| echo: false
#| out-width: "90%"
#| fig-cap: |
#|   The rendered output of the qmd file shown on the previous tab.

knitr::include_graphics("images/quarto_anatomy.png")
```

:::

:::

::: {.column width="50%"}

**Elements of a Quarto document include:**

::: {.fragment .highlight-current-red} 
1. An (optional) YAML header (surrounded by `---`s).
::: 

::: {.fragment .highlight-current-red} 
2. Plain text and any associated formatting. 
::: 

::: {.fragment .highlight-current-red} 
3. Chunks of code (surrounded by ```` ``` ```` s) and/or their output.
::: 

:::

::::

## Quarto Headers

The header of an .qmd file is a [YAML](https://en.wikipedia.org/wiki/YAML)^[You can read a bit more about YAML headers in Quarto [here](https://quarto.org/docs/get-started/hello/rstudio.html#yaml-header) and [this reference page](https://quarto.org/docs/reference/formats/html.html) lists all options possible for html output.]code block, and everything else is part of the main document. Try adding some of these other fields to your YAML and re-render it to see what it looks like. 

```{r}
#| eval: false
---
title: "Untitled"
author: "Victoria Sass"
date: "March 26, 2024"
output: html_document
---
```

. . . 

To mess with global formatting, [you can modify the header](http://rmarkdown.rstudio.com/html_document_format.html)^[Be careful though, YAML is space-sensitive; indents matter!]. 


```{r}
#| eval: false
output:
  html_document:
    theme: readable
```

## Quarto Syntax

:::: {.columns}
::: {.column width="50%"}
### Output

**bold/strong emphasis**
<br>
*italic/normal emphasis*
<br>
<br>
<h1 style="font-size:2.5em; color: #99a486"> Header </h1>
<br>
<h2 style="font-size:1.6em; "> Subheader </h2>
<br>
<h3 style="font-size:1.3em; "> Subsubheader </h3>

<br>

> Block quote from
> famous person
:::

::: {.column width="50%"}
### Quarto Syntax

```{default}
#| code-line-numbers: false
**bold/strong emphasis**
*italic/normal emphasis*
  
  
  
# Header
  
  
  
## Subheader
  


### Subsubheader
  



> Block quote from
> famous person
```

:::
::::

## Quarto Syntax^[This is all basic markdown syntax which you can learn about [here](https://quarto.org/docs/authoring/markdown-basics.html).] Continued

:::: {.columns}
::: {.column width="50%"}
### Output

1. Ordered lists
1. Are real easy
    1. Even with sublists
    1. Or with lazy numbering
  
* Unordered lists
* Are also real easy
  + Also even with sublists
    - And subsublists

:::

::: {.column width="50%"}
### Syntax
    
```{default}
#| code-line-numbers: false
1. Ordered lists
1. Are real easy
    1. Even with sublists
    1. Or with lazy numbering
  
    
    
    
    
* Unordered lists
* Are also real easy
  + Also even with sublists
    - And subsublists
```

:::
::::

## Formulae and Syntax

:::: {.columns}
::: {.column width="39%"}

### Output 

Include math $y= \left( \frac{2}{3} \right)^2$ inline. 

Or centered on your page like so: 

$$\frac{1}{n} \sum_{i=1}^{n} x_i = \bar{x}_n$$

Or write `code-looking font`.


Or a block of code:

```{r}
#| eval: false
#| code-line-numbers: false
y <- 1:5
z <- y^2
```
:::

::: {.column width="61%"}
### Syntax

````
Include math $y= \left(\frac{2}{3} \right)^2$ inline. 

Or centered on your page like so: 
  
$$\frac{1}{n} \sum_{i=1}^{n}x_i = \bar{x}_n$$


  
  
Or write`code-looking font`.

Or a block of code:

```{{r}}
y <- 1:5
z <- y^2
```

````

:::
::::

::: aside
Try copying any of the code chunks from the previous three slides to add some formatted text to your own qmd. 
:::

## Quarto Tinkering

Quarto docs can be modified in many ways. Visit these links for more information.

* Getting started with Quarto
  * [Tutorial: Hello, Quarto](https://quarto.org/docs/get-started/hello/rstudio.html)
  * [Tutorial: Computations](https://quarto.org/docs/get-started/computations/rstudio.html)
  * [Tutorial: Authoring](https://quarto.org/docs/get-started/authoring/rstudio.html)
* [Ways to modify the overall document appearance](https://quarto.org/docs/output-formats/html-basics.html)
* [Ways to format parts of your document](https://quarto.org/docs/authoring/markdown-basics.html)
* [Learn about the visual editor here](https://quarto.org/docs/visual-editor/)

## R Code in Quarto

Inside Quarto, lines of R code are called **chunks**. Code is sandwiched between sets of three backticks and `{r}`. This chunk of code...

````
```{{r}}
summary(cars)
```
````

Produces this output in your document:
```{r}
summary(cars)
```

. . . 

Add this code chunk to your document!

## Chunk Options

Chunks have options that control what happens with their code. They are specified as special comments at the top of a block. For example: 

````
```{{r}}
#| label: bar-chart
#| eval: false
#| fig-cap: "A line plot on a polar axis"
```
````

## Chunk Options

Some useful and common options include: 

* `echo: false` - Keeps R code from being shown in the document

* `eval: false` - Shows R code in the document without running it

* `include: false` - Hides all output but still runs code (good for `setup` chunks where you load packages!)

* `output: false` - Doesn't include the results of that code chunk in the output

* `cache: true` - Saves results of running that chunk so if it takes a while, you won't have to re-run it each time you re-render the document

* `fig.height: 5, fig.width: 5` - modify the dimensions of any plots that are generated in the chunk (units are in inches)

* `fig.cap: "Text"` - add a caption to your figure in the chunk

## Playing with Chunk Options

Try adding or changing the chunk options for the chunk in `my_first_Rmd.qmd` and re-render your document to see what happens.

```{r}
#| echo: fenced
#| eval: false
summary(cars)
```

## In-Line R code

Sometimes we want to insert a value directly into our text. We do that using code in single backticks starting off with `r`.


. . . 

```{r}
#| echo: false
library(knitr)
```

    Four score and seven years ago is the same as `r inline_expr("4*20 + 7", "md")` years.

. . . 

Four score and seven years ago is the same as `r 4*20 + 7` years.

. . . 

<br>

Maybe we've saved a variable in a code chunk that we want to reference in the text:

```{r}
x <- sqrt(77)
```

. . .

    The value of `x` rounded to the nearest two decimals is `r inline_expr("round(x, 2)", "md")`.

. . . 

The value of `x` rounded to the nearest two decimals is `r round(x, 2)`.

## This is Amazing!

Having R dump values directly into your document protects you from silly mistakes:

. . . 

* Never wonder "how did I come up with this quantity?" ever again: Just look at your formula in your .qmd file!

. . . 

* Consistency! No "find/replace" mishaps; reference a variable in-line throughout your document without manually updating if the calculation changes (e.g. reporting sample sizes).

. . . 

* You are more likely to make a typo in a "hard-coded" number than you are to write R code that somehow runs but gives you the wrong thing.

## Example: Keeping Dates

In your YAML header, make the date come from R's `Sys.time()` function by changing:

<br>

    date: "March 26, 2024"
  
to

    date: "`r inline_expr("Sys.time()", "md")`"

# Base `R` and Packages {.section-title background-color="#99a486"}

## Base `R`

Simply by downloading `R` you have access to what is referred to as Base `R`. That is, the built-in functions and datasets that `R` comes equipped with, right out of the box. 

. . . 

Examples that we've already seen include `<-`, `sqrt()`, `+`, `Sys.time()`, and `summary()` but there are obviously many many more. 

. . . 

You can see a whole list of what Base `R` contains by running `library(help = "base")` in the console. 

## A Base `R` Dataset: `cars`

In the sample Quarto document you are working on, we can load the built-in data `cars`, which loads as a dataframe, a type of object mentioned earlier. Then, we can look at it in a couple different ways.

. . . 

`data(cars)` loads this dataframe into the **Global Environment**.

```{r}
#| echo: false
data(cars)
```


. . . 

`View(cars)` pops up a **Viewer** tab in the source pane ("interactive" use only, don't put in Quarto document!). 

. . . 

```{r}
head(cars, 5) # prints first 5 rows, can use tail() too
```

## A Base `R` Dataset: `cars`

`str()` displays the structure of an object:
```{r}
str(cars) # str[ucture]
```

## A Base `R` Dataset: `cars`

`str()` displays the structure of an object:
```{r}
str(cars) # str[ucture]
```

`summary()` displays summary information ^[[Note R is **object-oriented**](https://adv-r.hadley.nz/oo.html) which means `summary()` provides different information for different types of objects!]:
```{r}
summary(cars)
```

## Base `R` is pretty...Basic

`hist()` generates a histogram of a vector. Note that you can access a vector that is a column of a dataframe using `$`, the **extract operator**.

::::{.columns}

:::{.column width="50%"}
```{r}
#| fig-width: 5
#| fig-height: 5.25
hist(cars$speed) # Histogram
```
:::

::: {.column width="50%"}
```{r}
#| fig-width: 5
#| fig-height: 5.25
hist(cars$dist)
```
:::
::::

## Base `R` is pretty...Basic 

We can try and make this histogram a bit more appealing by adding more arguments and their specifications. 

::: {.panel-tabset}

### Code

```{r}
#| code-line-numbers: (2-3)
#| eval: false
hist(cars$dist,
     xlab = "Distance (ft)", # X axis label
     main = "Observed stopping distances of cars") # Title
```

### Plot 

```{r}
#| fig-width: 5
#| fig-height: 5
#| fig-align: center
#| code-line-numbers: "2-3"
#| echo: false
hist(cars$dist,
     xlab = "Distance (ft)", # X axis label
     main = "Observed stopping distances of cars") # Title
```

:::

## Base `R` is pretty...Basic 

We can also make scatterplots to show the relationship between two variables. 

::: {.panel-tabset}

### Code

```{r}
#| code-line-numbers: "1"
#| eval: false
plot(dist ~ speed, data = cars,
     xlab = "Speed (mph)",
     ylab = "Stopping distance (ft)",
     main = "Speeds and stopping distances of cars",
     pch = 16) # Point shape
abline(h = mean(cars$dist), col = "firebrick") # add horizontal line (y-value)
abline(v = mean(cars$speed), col = "cornflowerblue") # add vertical line (x-value)
```

<br>

::: {.callout-important icon=false}

## <span style="color:red">{{< fa circle-exclamation >}}</span> Note
`dist ~ speed` is a formula of the type `y ~ x`. The first element (`dist`) gets plotted on the y-axis and the second (`speed`) goes on the x-axis. Regression formulae follow this convention as well!
:::

### Plot

```{r}
#| fig-width: 5
#| fig-height: 5
#| fig-align: center
#| echo: false
plot(dist ~ speed, 
     data = cars,
     xlab = "Speed (mph)",
     ylab = "Stopping distance (ft)",
     main = "Speeds and stopping distances of cars",
     pch = 16) # Point shape
abline(h = mean(cars$dist), col = "firebrick")
abline(v = mean(cars$speed), col = "cornflowerblue")
```

:::


## Base `R` is pretty...Basic 

We can also make scatterplots to show the relationship between two variables. 

::: {.panel-tabset}

### Code

```{r}
#| code-line-numbers: "3|5|6-7"
#| eval: false
plot(dist ~ speed, data = cars,
     xlab = "Speed (mph)",
     ylab = "Stopping distance (ft)", # add y-axis label
     main = "Speeds and stopping distances of cars",
     pch = 16) # Point shape
abline(h = mean(cars$dist), col = "firebrick") # add horizontal line
abline(v = mean(cars$speed), col = "cornflowerblue") # add vertical line
```

### Plot

```{r}
#| fig-width: 5
#| fig-height: 5
#| fig-align: center
#| echo: false
plot(dist ~ speed, 
     data = cars,
     xlab = "Speed (mph)",
     ylab = "Stopping distance (ft)",
     main = "Speeds and stopping distances of cars",
     pch = 16) # Point shape
abline(h = mean(cars$dist), col = "firebrick")
abline(v = mean(cars$speed), col = "cornflowerblue")
```

:::

## Another Base `R` Dataset: `swiss`

Let's look at another built-in dataset. 

. . . 

First, run `?swiss` in the console to see what things mean.

. . . 

Then, load it using `data(swiss)`

. . . 

Add chunks to your Quarto document inspecting `swiss`, defining variables, doing some exploratory plots using `hist` or `plot`.

You might experiment with [colors](https://r-charts.com/colors/) and [shapes](https://r-charts.com/base-r/pch-symbols/). 

## Looking at `swiss`

:::{.panel-tabset}

### Code

```{r}
#| code-line-numbers: "|1"
#| eval: false
pairs(swiss, 
      pch = 8, 
      col = "violet",
      main = "Pairwise comparisons of Swiss variables")
```

### Plot

```{r}
#| fig-width: 4.75
#| fig-height: 4.75
#| fig-align: center
#| echo: false
pairs(swiss, 
      pch = 8, 
      col = "violet",
      main = "Pairwise comparisons of Swiss variables")
```

:::

::: aside
pairs() is a pairwise scatterplot function. Good for a quick look at small datasets with numerical/continuous data, but mostly useless for larger data.
:::

## Packages

What makes `R` so powerful though is it's extensive library of **packages**. Due to it's open-source nature, anyone (even you!) can write a package that others can use. 

. . . 

Packages contain pre-made functions and/or data that can be used to extend Base `R`'s capabilities. 

. . . 

::: {.callout-note icon=false}

## <span style="color:blue">{{< fa circle-info >}}</span> \ Base `R`/Package Analogy
Base `R` is like creating a recipe from scratch: going to the store and buying all the ingredients and cooking it by yourself. Using a package is more akin to using a meal-kit service: you still have to cook but you're provided with the ingredients and step-by-step instructions for making the recipe. 
:::

. . . 

As of this writing there are 20,613^[To put this in perspective, there were 19,940 available packages the last time I taught this course (Fall 2023).] [available packages](https://cran.rstudio.com/)!

## Installing Packages

To use a package outside of Base `R` you need to do two things: 

## Installing Packages

To use a package outside of Base `R` you need to do two things: 

1. Download the package from `CRAN` (The `C`omprehensive `R` `A`rchive `N`etwork) by running the following in your **console:**^[You never want to include this line of code in a Quarto document or an R Script]

```{r}
#| eval: false
#| code-line-numbers: false
install.packages("package_name")
```

. . . 

## Installing Packages

To use a package outside of Base `R` you need to do two things: 

1. Download the package from `CRAN` (The `C`omprehensive `R` `A`rchive `N`etwork) by running the following in your **console:**^[You never want to include this line of code in a Quarto document or an R Script]

```{r}
#| eval: false
#| code-line-numbers: false
install.packages("package_name")
```

This downloads the package to your local machine (or the server of whatever remote machine you're using). Thus, you only every need to do it once for each package^[You'll only need to re-install a package when you update `R` or if the package itself comes out with an updated version with new features you want to use.]!

## Installing Packages

To use a package outside of Base `R` you need to do two things: 

1. Download the package from `CRAN` (The `C`omprehensive `R` `A`rchive `N`etwork) by running the following in your **console**^[You never want to include this line of code in a Quarto document or an R Script]:

```{r}
#| eval: false
#| code-line-numbers: false
install.packages("package_name")
```

This downloads the package to your local machine (or the server of whatever remote machine you're using). Thus, you only every need to do it once for each package^[You'll only need to re-install a package when you update `R` or if the package itself comes out with an updated version with new features you want to use.]!

2. Once a package is installed, you need to load it into the current session of `R` so you can use it. You'll do this by putting the following in an `R` Script or embedded in a code chunk in a Quarto file: 

```{r}
#| eval: false
library(package_name)
```

## `gt` Package

Let's make a table that's more polished than the code-y output `R` automatically gives us. To do this, we'll want to install our first **package** called `gt`. 
In the **console**, run: `install.packages("gt")`.

::: {.callout-caution icon=false}
## <span style="color:tomato">{{< fa triangle-exclamation >}}</span> Different Syntax
Notice that unlike the `library()` command, *the name of a package to be installed must be in quotes*? This is because the name here is a search term (text, not an object!) while for `library()` it is an actual R object.
:::

## Making cleaner tables 

::: {.panel-tabset}

### Code

```{r}
#| eval: false
#| code-line-numbers: "|1|"
library(gt) # loads gt, do once in your session
gt(as.data.frame.matrix(summary(swiss))) 
```


::: {.fragment}
::: {.callout-tip icon=false}
## <span style="color:green">{{< fa note-sticky >}}</span> Nesting Functions
Note that we put the `summary(swiss)` function call inside the `as.data.frame.matrix()` call which all went into the `gt()` function. This is called *nesting functions* and is very common. I'll introduce a method next week to avoid confusion from nesting too many functions inside each other.
:::
:::

::: {.fragment}
::: {.callout-note icon=false}
## <span style="color:blue">{{< fa info-circle >}}</span> What's `as.data.frame.matrix()` Doing?
`gt()` takes as its first argument a `data.frame`-type object, while `summary()` produces a `table`-type object. Therefore, `as.data.frame.matrix()` was additionally needed to turn the `table` into a `data.frame`.
:::
:::

### Table
```{r}
#| echo: false
library(gt) # loads gt, do once in your session
swiss |> 
  summary() |> 
  as.data.frame.matrix() |> 
  gt() |> 
  tab_options(table.align = "center", 
              table.font.size = pct(75)) 
```
:::

## `gt`'s Version of `head()` and `tail()`

::: {.panel-tabset}

### `head()`

```{r}
head(swiss)
```

### `gt_preview()` alternative

```{r}
#| eval: false
gt_preview(swiss, 
           top_n = 3, # default is 5
           bottom_n = 3) # default is 1 
```

```{r}
#| echo: false
swiss |> 
  gt_preview(top_n = 3, bottom_n = 3) |> 
  tab_options(table.align = "center", table.font.size = pct(70))
```

:::

::: {.fragment}
::: {.callout-note icon=false}
## 👋 Bye Bye `as.data.frame.matrix()` 
We no longer need `as.data.frame.matrix()` since we're no longer using `summary()`. Both `head()` and `gt_preview()` take a `data.frame`-type object as their first argument which is the same data type as `swiss`. 
:::
:::

# Homework{.section-title background-color="#1e4655"}

## {data-menu-title="Homework 1" background-iframe="https://vsass.github.io/CSSS508/Homework/HW1/homework1.html" background-interactive=TRUE}

## {data-menu-title="Lecture Resources" background-iframe="https://vsass.github.io/CSSS508/Lectures/Lecture1/CSSS508_Lecture1_index.html" background-interactive=TRUE}