```{r, echo = FALSE}
library(knitr)
opts_chunk$set(comment = "")
```

## Welcome!

1. Introductions
2. Topics overview
3. Getting R up and running


```{r, fig.alt="Welcome!", out.width = "60%", echo = FALSE, fig.align='center'}
knitr::include_graphics("images/welcome.jpg")
```

<sub>[Photo by <a href="https://unsplash.com/@bel2000a?utm_source=unsplash&utm_medium=referral&utm_content=creditCopyText">Belinda Fewings</a> on <a href="https://unsplash.com/s/photos/welcome?utm_source=unsplash&utm_medium=referral&utm_content=creditCopyText">Unsplash</a>]</sub>
  
## About Us

**Ava Hoffman (she/her)**

Senior Staff Scientist, Fred Hutchinson Cancer Center

Associate, Department of Biostatistics, JHSPH

PhD in Ecology

Email: ahoffma2@fredhutch.org  Web: https://avahoffman.com

```{r, fig.alt="Ava's picture", out.width = "30%", echo = FALSE, fig.align='center'}
knitr::include_graphics(here::here("modules", "Day_1", "images", "ava.png"))
```

## About Us

**Carrie Wright (she/her)** 

Senior Staff Scientist, Fred Hutchinson Cancer Center

Associate, Department of Biostatistics, JHSPH

PhD in Biomedical Sciences

Email: cwright2@fredhutch.org  Web: https://carriewright11.github.io

```{r, fig.alt="Carrie's picture", out.width = "30%", echo = FALSE, fig.align='center'}
# knitr::include_graphics("https://ca.slack-edge.com/T023TPZA8LF-U024F9G49S8-9861ddd543db-192")
knitr::include_graphics(here::here("modules", "Day_1", "images", "carrie.png"))
```

## The Learning Curve

Learning a programming language can be very intense and sometimes overwhelming.

We recommend fully diving in and making lots of mistakes through trial and error.

We want you to succeed -- We will get through this together!

```{r, fig.alt="Sweeping the ocean", out.width = "25%", echo = FALSE, fig.align='center'}
knitr::include_graphics("images/sweeping-the-ocean.gif")
```

## What is R?

- R is a language and environment for statistical computing and graphics developed in 1991

- R is both [open source](https://en.wikipedia.org/wiki/Open_source) and [open development](https://en.wikipedia.org/wiki/Open-source_software_development) (aka, free!)

```{r, fig.alt="R logo", out.width = "20%", echo = FALSE, fig.align='center'}
knitr::include_graphics("https://www.r-project.org/Rlogo.png")
```

- Powerful and flexible - especially for data wrangling and visualization

- Extensive add-on software (packages)

- Strong community -- https://rladies.org/

<sub>[source: http://www.r-project.org/, https://en.wikipedia.org/wiki/R_(programming_language)]</sub>

## Workshop Website

https://hutchdatascience.org/SeattleStatSummer_R/

```{r, fig.alt="Intro to R course logo", out.width = "60%", echo = FALSE, fig.align='center'}
knitr::include_graphics("../../docs/images/Intro_to_R.png")
```

## Learning Objectives

- Understanding basic programming syntax
- Reading data into R
- Summarizing and grouping data
- Filtering data
- Recoding data
- Making plots with your data

## Installing R

* Install the [latest R version](http://cran.r-project.org/) `r config::get("r_version")`

* [Install RStudio](https://www.rstudio.com/products/rstudio/download/)

More detailed instructions [on the website](https://jhudatascience.org/intro_to_r/docs/module_details/day0.html).

RStudio is an **integrated development environment** (IDE) that makes it easier to work with R.

More on that soon!

## Getting files from downloads

This course will involve moving files around on your computer and downloading files.

If you are new to this - check out these videos.

If you have a PC: https://youtu.be/we6vwB7DsNU

If you have a Mac: https://www.youtube.com/watch?v=Ao9e0cDzMrE

You can find these on the resource page of the website.

## Useful (+ mostly Free) Resources

Found on our website under the `Resources` tab:
https://hutchdatascience.org/SeattleStatSummer_R/resources.html

-  videos from our Intro to R Course
-  cheatsheets from that course

## Useful (+ mostly Free) Resources {.small}

**Want more?**  

- Tidyverse Skills for Data Science Book: https://jhudatascience.org/tidyversecourse/ 
(more about the tidyverse, some modeling, and machine learning)

- Tidyverse Skills for Data Science Course: https://www.coursera.org/specializations/tidyverse-data-science-r  
(same content with quizzes, can get certificate with $)

- R for Data Science: http://r4ds.had.co.nz/  
(great general information)

- R basics by Rafael A. Irizarry: https://rafalab.github.io/dsbook/r-basics.html
(great general information)
 
- Open Case Studies: https://www.opencasestudies.org/  
(resource for specific public health cases with statistical implementation and interpretation)

- Dataquest: https://www.dataquest.io/  
(general interactive resource)

## Useful (+ mostly Free) Resources

**Need help?** 

- Various "Cheat Sheets": https://www.rstudio.com/resources/cheatsheets/   

- R reference card: http://cran.r-project.org/doc/contrib/Short-refcard.pdf  

- R jargon: https://link.springer.com/content/pdf/bbm%3A978-1-4419-1318-0%2F1.pdf  

- R vs Stata: https://link.springer.com/content/pdf/bbm%3A978-1-4419-1318-0%2F1.pdf  

- R terminology: https://cran.r-project.org/doc/manuals/r-release/R-lang.pdf

## Summary

- R is a powerful data visualization and analysis software language.
- Lots of **resources** can be found on the website.

🏠 [Workshop Website](https://hutchdatascience.org/SeattleStatSummer_R/)