2019_07_JSM_DataScience.Rmd

---
title: 'Sharpening the Tools in Your Data Science Toolbox `r icon::fa("toolbox")`'
author: "Jessica Minnier, PhD<br><span style = 'font-size: 50%;'>OHSU-PSU School of Public Health<br>Knight Cancer Institute Biostatistics Shared Resource<br>Oregon Health & Science University</span>"
date: '[Joint Statistical Meetings](https://ww2.amstat.org/meetings/jsm/2019/onlineprogram/ActivityDetails.cfm?sessionid=218337), July 29, 2019<br><br>`r icon::fa("link")` [bit.ly/jmin-jsm19](https://bit.ly/jmin-jsm19)<br>`r icon::fa("twitter")` [datapointier](https://twitter.com/datapointier)'
output:
  xaringan::moon_reader:
    css: [css/xaringan-themer.css, css/my-theme.css]
    lib_dir: libs
    nature:
      countIncrementalSlides: false
      titleSlideClass: ["left", "middle", "inverse"]
      highlightLines: true
      highlightStyle: solarized-dark
      ratio: "16:9"
    includes:
      in_header: ../libs/header.html
---

layout: true
  
<div class="my-footer"><span>bit.ly/jmin-jsm19</span></div> 


---

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

library(tidyverse)

knitr::opts_chunk$set(
  warning=FALSE, 
  message=FALSE, 
  fig.width=10.5, 
  fig.height=4, 
  comment=NA, 
  rows.print=16,
  echo=FALSE)
theme_set(theme_bw(base_size = 24))
```


```{r xaringan-themer, include = FALSE}
# devtools::install_github("gadenbuie/xaringanthemer")
library(xaringanthemer)
mono_light(
  base_color =  "#3A6185", #5e97c9" ## OHSU Marquam, #"#125972" ## picked to coordinate with rOpenSci logo 
  code_highlight_color = "#c0e8f5",
  link_color = "#38BDDE",
  header_font_google = google_font("Josefin Sans"),
  text_font_google   = google_font("Montserrat", "300", "300i"),
  code_font_google   = google_font("Droid Mono"),
  text_font_size = "26px",
  outfile = "css/xaringan-themer.css"
  # title_slide_background_image = "img/CAN-RGB-4C-REV.png",
  # title_slide_background_position = "80% 60%",
  # title_slide_background_size = "400px" #"40%"
)
```


class: inverse, middle

# Who am I?

- Use R every day, git often, unix sometimes, python rarely
- Teach intro to R, R markdown, intro to stats for data science, R Shiny (and Math/Stats)
- Collaborative statistician (mostly applied work, no PhD students, no Postdocs, some MS students and staff)
- Involved in: organizing Cascadia R conf, PDX R Meetup, R Ladies, BioData Club

---

# Statistics is changing

A non-random sample of buzzwords:

- Big Data
- Data Science
- Machine Learning
- Reproducible Coding
- Version Control
- Interactive Dashboards



---

<center><img src="img/asa_statement_datasci.png" width="80%"/></center>

> Sustained and substantial collaborative effort with researchers with expertise in data organization and in the flow and distribution of computation. <font color="red">Statisticians must engage them, learn from them</font>, teach them, and work with them.

> Statistical <font color="red">education and training must continue to evolve</font>—the next generation of statistical professionals needs a <font color="red">broader skill set</font> and must be more able to engage with database and distributed systems experts. 

> The next generation must include more researchers with skills that <font color="red">cross the traditional boundaries of statistics</font>, databases, and distributed systems; there will be an ever-increasing demand for such “multi-lingual” experts.

---

# Programming itself is changing

- Data Science is programming intensive
  + Big data and complex models (machine learning beyond regression)
- Beyond SAS
  + R is easier to learn than ever before (see: tidyverse)
  + R packages are easier to make and distribute
  + R is not "slow" anymore
  + [FDA allows R](https://blog.revolutionanalytics.com/2012/06/fda-r-ok.html) for clinical trials
- Python is most common in data science
  + but not statistics!

---

## Data Science Jobs: Python, SQL, .... R

.pull-left[
<center><img src="img/r4stats_popularity_jobs.png" width="100%"/></center>
[R4stats - Robert A. Muenchen](http://r4stats.com/articles/popularity/)
]
.pull-right[
<center><img src="img/r4stats_popularity_jobs_pct.png" width="100%"/></center>
]

---

## By contrast, scholarly articles: SPSS, R, SAS

.pull-left[
<center><img src="img/r4stats_popularity_articles.png" width="90%"/></center>
]
.pull-right[
<center><img src="img/r4stats_popularity_articles_trend.png" width="98%"/></center>
[R4stats - Robert A. Muenchen](http://r4stats.com/articles/popularity/)
]

---


.pull-left-40[

## How to keep up?
Learning takes time, dedication, courage.
]

.pull-right-60[
<center><img src="img/draw_owl.png" width="100%"/></center>
]


---
## Highlights of my education in programming
.pull-left[
CS courses in college (C, Java):
<img src="img/college_cs2.png" width="100%"align="top"/>
My PhD advisor wrote a *ton* of code and functions, shared it all with me.
<img src="img/library_gradschool.png" width="100%"align="top"/>
]
.pull-right[
Postdoc (learned git/github):
<img src="img/softwarecarp.png" width="100%"align="top"/>

First year Assistant Professor (R Markdown, Shiny were all new & exciting!)
<img src="img/user2014.png" width="100%"align="top"/>
]

---

## Learning while teaching

<img src="img/pres1.png" width="35%"align="top"/><img src="img/pres2.png" width="30%"align="top"/><img src="img/pres3.png" width="35%"align="top"/>
<img src="img/pres4.png" width="28%"align="top"/><img src="img/pres5.png" width="36%"align="top"/><img src="img/pres6.png" width="36%"align="top"/>
[github.com/jminnier/talks_etc](https://github.com/jminnier/talks_etc)

---

## Learning while teaching with new tools

(also: find collaborators better than you at all this - thanks [Ted Laderas!]())

<img src="img/teach1.png" width="27%"align="top"/><img src="img/teach2.png" width="33%"align="top"/><img src="img/teach3.png" width="33%"align="top"/> 

###### [r-bootcamp.netlify.com](https://r-bootcamp.netlify.com/); [minnier.shinyapps.io/ODSI_categoricalData/](https://minnier.shinyapps.io/ODSI_categoricalData); [minnier.shinyapps.io/ODSI_continuousData](https://minnier.shinyapps.io/ODSI_continuousData/)

---

# Software development

.pull-left[
- Unix/shell (i.e. for cluster computing)
- Programming skills
- Version control (i.e. git/github/gitlab, bitbucket)
- Unit Testing (does your code work?)
- Collaborative coding
- Using databases (i.e. SQL)
- Automation (i.e. make)
]
.pull-right[
<img src="img/softwarecarp.png" width="100%" align="top"/>
https://software-carpentry.org/

<img src="img/whattheyforgot.png" width="100%" align="top"/>
https://whattheyforgot.org/
]

---

# Improve your coding skills

### Similar to learning a new language

- Difficult to do when busy/sporadically, unless you set aside time (make a deadline) or find an immersive experience
- Learn more R? SAS/STATA? Find workshops! (JSM, CSP, SDSS, Rstudio::conf, UseR!, local R meetups and conferences)
- Learn git/github/software development? Host a [Software Carpentry](https://software-carpentry.org/) workshop

<img src="img/sdss2020.png" width="25%"align="top"/><img src="img/rstudioconf2020.png" width="35%"align="top"/>
<img src="img/rstudioconfworkshop.png" width="35%"align="top"/>


---
layout: false

## Coding in R is more fun these days

- R Markdown $\to$ reproducible documents
  + transformative for collaborative statistical analyses
  + these slides are made with knitr/r markdown
  + make textbooks, webpages, much more
- Shiny $\to$ webpages to show off methodology/analyses

<center><img src="img/horst_rmarkdown_wizards.png" width="47%" height="50%" align="top"><img src="img/horst_ggplot2_masterpiece.png" width="41%" height="50%" align="top"><a href="https://github.com/allisonhorst/stats-illustrations"><br>Allison Horst</a></center>


---

# Find a community & learn together
.pull-left[

We all have something to learn!

- Meetup groups (R Users, R Ladies, Women Who Code)
- Hackweeks 
- Data Science Workshops
- Data competitions (DataFest)
- Workshops at conferences
- Online: [#rstats Twitter](https://twitter.com/hashtag/rstats?src=hash), [Rstudio community](https://community.rstudio.com/), 
[R 4 Data Science Learning community](https://www.rfordatasci.com/), [Tidy Tuesday](https://github.com/rfordatascience/tidytuesday)
- Start your own club!
]
.pull-right[
<img src="img/biodataclub1.png" width="70%" align="top">

https://biodata-club.github.io/
]

---
## It takes time to learn how to learn

.pull-left[

#### R specific learning checks from Alison Hill's [Big Magic with R: Creative Learning Beyond Fear](https://alison.rbind.io/talk/2018-cascadia-bigmagic/) - watch the [video](https://www.youtube.com/watch?v=seERGgG6uVs&list=PLxHlPKedTUbL7ckoP5Elrdrw64V7o5_h6&index=3&t=0s)!
<img src="img/hill_magic.png" width="95%" align="top">

]
.pull-right[
<img src="img/hill_learn.png" width="100%">
]


---

## Practice, practice, practice

- Learning a tool and then forgetting to use it is the best way to unlearn it
- Write down what you've learned (make a list of commands, write a blog post)

## Give talks

- Sign up to give talks at local meetups
- Teach workshops to students/fellow faculty/coworkers
- Journal/book clubs with your co-workers/team

---

.pull-left[

## Resources $\rightarrow$

- Interactive lessons
- Online courses
- Blog posts

## Ask for help

- Stack Overflow
- Rstudio Community

]
.pull-right[
<center><a href="https://github.com/jminnier/awesome-rstats/"><img src="img/jminnier_learnr.png" width="100%" height="50%">github.com/jminnier</a></center>
]
---


.pull-left[
# We don't want to be left behind

- Work on projects outside of your comfort zone
- Grow as statisticians, grow as a field
- Be open to other fields collaborating on "data science"
]
.pull-right[
# Don't forget to have fun!

<center><img src="img/horst_welcome_to_rstats_twitter.png" width="95%" height="50%"><a href="https://github.com/allisonhorst/stats-illustrations"><br>Allison Horst</a></center>

]

---
class: inverse

# Thank you!

.pull-left-60[

Contact me: `r icon::fa("envelope")` minnier-[at]-ohsu.edu, `r icon::fa("twitter")` [datapointier](https://twitter.com/datapointier), `r icon::fa("github")` [jminnier](https://github.com/jminnier/)

Slides available: [bit.ly/jmin-jsm19](https://bit.ly/jmin-jsm19)

Slide code and files available at: [github.com/jminnier/talks-etc](https://github.com/jminnier/talks_etc)


Slides created via the R package [xaringan](https://github.com/yihui/xaringan) by [Yihui Xie](https://twitter.com/xieyihui?lang=en) with the [xaringanthemer](https://github.com/gadenbuie/xaringanthemer) package by [Garrick Aden-Buie](https://github.com/gadenbuie), inspired by slides and slide formatting by [Alison Hill](https://alison.rbind.io/), [Jennifer Thompson](https://jenthompson.me/), and [Chester Ismay](https://ismayc.github.io/)
]
.pull-right-40[
<center><img src="img/horst_r_first_then.png" width="100%" height="50%"><a href="https://github.com/allisonhorst/stats-illustrations"><br>Allison Horst</a></center>
]