WHO AM I?

Mark Scheuerell

Assistant Unit Leader

U.S. Geological Survey Washington Cooperative Fish and Wildlife Research Unit


Associate Professor

School of Aquatic and Fishery Sciences

My role as course instructor

  • Help you learn the material
  • Help you learn how to ask for help
  • Be a future resource

My role as course instructor

  • I plan to fail
  • A lot
  • In public

WHO ARE YOU?

Introduce yourself

  1. Your school/department

  2. Your area of study

  3. Something you’re excited to learn this quarter

Software requirements

Software in this course

  1. Is free

  2. Is well supported by the user community

R Software

An environment for statistical computing and graphics

R packages

Most of R’s current capabilities come from packages

  • We’ll use a variety of them for many different tasks
  • We’ll also learn how to create our own!

RStudio

An integrated development environment (IDE) for R

  • Syntax highlighting, code completion, smart indentation
  • Easily manage multiple working directories using projects
  • Extensive package development tools
  • Built-in tools & GUIs for Git & R Markdown

 

RStudio benefits

 

GitHub

Cloud-based code repository & collaboration platform

  • Store, manage, track changes to code
  • Communicate with other team members
  • Uses Git for version control

 

 

Git

Version control system (VCS)

Git records changes to a file or set of files over time so that you can recall specific versions later

PostgreSQL

Open source relational database system

  • Uses & extends the SQL language
  • Highly extensible (eg, define your own data types)
  • Active user community

R Markdown

Notebook interface to weave together text, equations, and code into nicely formatted output

Allows you to create and document fully reproducible workflows

R Markdown

Supports dozens of static and dynamic output formats

  • HTML
  • PDF
  • MS Word
  • HTML5 slides
  • Books
  • Shiny apps
  • Scientific articles
  • websites

Gallery here