NEON @ ESA: Work with Ecological Time Series Data in R

August 07, 2016
Ecological Society of America Annual Meeting

This 3.5-hr workshop, taught at the 2016 meeting of the Ecological Society of America (ESA) in Ft. Lauderdale, FL, will cover how to open, work with and plot tabular (.csv format) time-series data in R. Additional topics include working with time and date classes (e.g., POSIXct, POSIXlt, and Date), subsetting time series data by date and time, and created facetted or tiles sets of plots. All materials taught in this workshop were developed in collaborative effort between Data Carpentry and the National Ecological Observatory Network (NEON).

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 workshop will be taught at the 2016 meeting of the Ecological Society of America (ESA) in Ft. Lauderdale, FL. You must be a registered attendee of the conference and register for this workshop to participate in this workshop. For more information, visit the ESA 2016 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 at the bottom of this page.

Install R Packages

Please have these packages installed and updated prior to the start of the workshop. * ggplot2: install.packages("ggplot2") * lubridate: install.packages("lubridate") * scales: install.packages("scales") * gridExtra: install.packages("gridExtra") * reshape2: install.packages("reshape2") * zoo: install.packages("zoo")

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

Download NEON Teaching Data Subset: Meteorological Data for Harvard Forest

The data used in this lesson were collected at the National Ecological Observatory Network's Harvard Forest field site. These data are proxy data for what will be available for 30 years on the NEON data portal for the Harvard Forest and other field sites located across the United States.

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.

Workshop Instructors

  • Megan A. Jones; @meganahjones, Staff Scientist/Science Educator; NEON program, Battelle
  • Samantha Weintraub; @sr_weino, Staff Scientist, Terrestrial Biogeochemist; NEON program, Battelle

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

Social Media

Please tweet @NEON_sci and using the hashtag #WorkWithData during this workshop!

Workshop Location

Location: Ft Lauderdale Convention Center, Rm 316 Please double check the conference schedule as rooms may change!

All online materials can be accessed and used after the workshop and are linked on the next page: Workshop Materials in menu bar.


Additional Set Up Instructions

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

Setting Up R & RStudio

Windows R/RStudio Setup

Once R and RStudio are installed, click to open RStudio. If you don't get any error messages you are set. If there is an error message, you will need to re-install the program.

Mac R/RStudio Setup

  • If your Mac is set up for UiO use, you can install R from Managed Software Center

  • Go to CRAN and click on Download R for (Mac) OS X

  • Select the .pkg file for the version of OS X that you have and the file will download.
  • Double click on the file that was downloaded and R will install
  • Go to the RStudio Download page
  • Under Installers select RStudio 0.98.1103 - Mac OS X 10.6+ (64-bit) to download it.
  • Once it's downloaded, double click the file to install it

Once R and RStudio are installed, click to open RStudio. If you don't get any error messages you are set. If there is an error message, you will need to re-install the program.

Linux R/RStudio Setup

  • R is available through most Linux package managers. You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo yum install R).
  • To install RStudi, go to the RStudio Download page
  • Under Installers select the version for your distribution.
  • Once it's downloaded, double click the file to install it

Once R and RStudio are installed, click to open RStudio. If you don't get any error messages you are set. If there is an error message, you will need to re-install the program.

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h2 id="set-wd">Set Working Directory to Downloaded Data

1) Download Data

After clicking on the Download Data button, the data will automatically download to the computer.

2) Locate .zip file

Second, find the downloaded .zip file. Many browsers save downloaded files to your computer’s Downloads directory. If you have previously specified a specific directory (folder) for downloaded files, the .zip file will download there.

3) Move to **data** directory

Third, move the downloaded file to a directory called data within the Documents directory on your computer. You can choose to place the data in other locations, however, you will need to remember to set your R Working Directory to that location and not as we demonstrate in the workshop.

4) Unzip/uncompress

Fourth, we need to unzip/uncompress the file so that the data files can be accessed. Use your favorite tool that can unpackage/open .zip files (e.g., winzip, Archive Utility, etc). The files will now be accessible in three directories:

These directories contain all of the subdirectories and files that we will use in this workshop.

5) Set working directory

Fifth, we need to set the working directory in R to this data directory that is parent to the directories containing the data we want. For complete directions, on how to do that check out the Set A Working Directory in R tutorial.

Time Topic
7:45 Please come early if you have any setup or installation issues
8:00 Intro to Time Series Data in R
9:00 Dealing With Dates & Times in R
9:30 --------- BREAK ---------
9:45 NoData Values & Subsetting by Date
10:10 Time Series Plots with ggplot2
10:40 Multi-panel Plots with ggplot Facets
11:15 Additional Questions & Evaluation
11:30 End

Series: Introduction to Working With Time Series Data in Text Formats in R

You can choose to do this optional data activity (opens in a new window), or continue to the next lesson plan.

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