Environmental Data Analysis and Visualization

Documenting for Future Users (and Future You)

Visualization critique

nih.gov

Visualization critique

eia.gov

Next visualization critiques

  • Megan

  • Sierra

  • Tommy

Sensor of the Day

Passive acoustic monitoring

Sensor of the Day

Passive acoustic monitoring

Goulette et al. 2021 “Opportunistic Acoustic Telemetry Platforms” NOAA

NOAA NCEI Passive Acoustic Data

Sensor of the Day

Sensor of the Day

Sensor of the Day

Quarto

Quarto is a data science documentation and publishing system that comes built-in to RStudio.

http://quarto.org

Reproducibility in data science

The Turing Way project illustration by Scriberia. CC-BY 4.0 DOI: 10.5281/zenodo.3332807.

Isn’t code reproducible by default?

Code will do precisely what we want, but it will not necessarily understood by others.

Isn’t code reproducible by default?

Literate programming

An approach to writing software that centers the human user (and re-user) by combining natural language explanations with code.

https://akkartik.name/post/literate-programming

Code notebooks

A code notebook is software tool for literate programming.

Communicating beyond the notebook

Presentations

Websites

Interactive Visualizations

Working on a workflow

Code notebooks provide a convenient way to document and organize a data science project from beginning to end; in otherwords, they can form the basis of a workflow.

Working on a workflow

Working on a workflow

Working on a workflow

Working on a workflow

What about files?

When we write code that reads from files, these need to be in places where the Quarto document can find them.

# load tidyverse
library(tidyverse)
# read in abalone data
abalone<-read_csv("data/abalone.csv")
# plot abalone rings by diameter
ggplot(abalone,aes(x=diameter,y=rings)) +
  geom_hex()

Sharing your file system

The zip function provides a convenient way to turn your entire working directory into a .zip file

#zip up all of my project files
zip("myProject.zip",list.files())

Coursekeeping

Assignment Due Date
Coding Assignment 1 Wednesday, October 9
Lab Assignment 6 Monday, October 14
Project Proposal Friday, October 18
Lab Assignment 7 Monday, October 21

Project proposal

  • What is the topic?

  • What is the background to this topic? (2-3 citations)

  • What datasets are you intending to use?

  • How would data analysis/visualization to help you understand the topic?

  • Suggest two visualizations

Activity: Brainstorming with Quarto

Put the Quarto workflow to work in brainstorming ideas for your final project!

  • Create a file system for your final project

  • Start a new Quarto document and save it to your working directory

  • Use headers to outline a data analysis process from a project you’d like to do.

  • Begin filling out the sections with some preliminary ideas about what kinds of data you’d useand

    • Use links to promising datasets in the text

    • Use code chunks with comments to draft code

Next week

  • Working with messy data

  • Exploring the tidyverse

  • Data transformations using dplyr