Workshop

Working with Time Series in R using NEON Data | ESA 2017

Ecological Society of America Annual Meeting

The temporal scale of ecological research is expanding given increased continental and global availability of time series data coming from long term data collection efforts such as NEON, LTER and Fluxnet. Given increased data availability, there is a need to implement efficient, well-documented and reproducible workflows in tools like R.

This workshop will teach participants how to import, manipulate, format and plot time series data stored in .csv format in R while working with NEON data. We will work with temperature and phenology data to explore working with and visualizing data with different time scale intervals. Key skills learned will include:

  1. working with data.frames in R (dplyr package),
  2. converting timestamps stored as text strings to R date or datetime (e.g. POSIX) classes (lubridate package),
  3. aggregating data across different time scales (day vs month) and
  4. plotting time series data (ggplot2 package).

Required Prior Knowledge

The workshop will assume that participants have a basic level of familiarity with working with data in R, including installing and loading packages, and data import.

This 5-hr workshop will be taught at the 2017 meeting of the Ecological Society of America (ESA) in Portland, OR. You must be a registered attendee of the conference and register for this workshop with your ESA registration to participate in this workshop. For more information, visit the ESA 2017 annual meeting website.

Things You’ll Need For The Workshop

To participant in this workshop, you will need a laptop with the most current version of R, and preferably RStudio, loaded on your computer.

For details on setting up RStudio in Mac, PC, or Linux operating systems please see the instructions below.

Install R Packages

Please have these packages installed and updated prior to the start of the workshop.

  • dplyr: install.packages("dplyr")
  • ggplot2: install.packages("ggplot2")
  • lubridate: install.packages("lubridate")
  • scales: install.packages("scales")
  • tidyr: install.packages("tidyr")
  • gridExtra: install.packages("gridExtra")

Updating R Packages

In RStudio, you can go to Tools --> Check for package updates to update previously installed packages on your computer.

Or you can use update.packages() to update all packages that are installed in R automatically.

More on Packages in R

Download Data

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Once you have downloaded the data, please set up a "data" directory as a parent directory to these three uncompressed directories. Set your R working directory to this "data" directory prior to the beginning of the workshop. If you would like further instruction please see the bottom of this page for detailed instructions.

Workshop Instructors

  • Megan A. Jones; @meganahjones, Staff Scientist/Science Educator; NEON program, Battelle
  • Natalie Robinson; Staff Scientist, Quantitative Ecologist; NEON program, Battelle
  • Lee Stanish; Staff Scientist, Microbial Ecologist; NEON program, Battelle

Please get in touch with the instructors prior to the workshop with any questions.

Twitter?

Please tweet using the hashtag #WorkWithData & @NEON_Sci during this workshop!

Charging Station

ESA has informed us there will not be power available at each table. However, there will be a charging station in the room. If you are concerned about battery during the workshop, consider reducing your screen brightness at the start of the workshop.

Before the Workshop

Prior to the workshop you should have R and, preferably, RStudio installed on your computer.

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Workshop Schedule

Location: C125-126, Oregon Convention Center

Please double check the conference schedule as rooms can change!

Please note that the schedule listed below may change depending upon the pace of the workshop!

Time Topic
11:45 Please come early if you have any setup or installation issues.
12:00 Working With NEON Phenology Data - Discrete Time Series
13:30 --------- BREAK 1 ---------
13:45 Working with NEON Temperature Data - Continuous Time Series
15:00 --------- BREAK 2 ---------
15:15 Combining Discrete & Continuous Time Series in Plotting
16:30 Final Questions & Evaluation

Twitter?

Please tweet using the hashtag #WorkWithData & @NEON_Sci during this workshop!

Online Tutorials

All NEON workshops and self-paced tutorials can be accessed via the NEON Data Skills educational resources.