NEON EDUCATION bio photo

NEON EDUCATION

Devoted to open data and open source in science and education.

View All Tutorials

Tags

R programming (52)
Hierarchical Data Formats (HDF5) (15)
Spatial Data & GIS (22)
LiDAR (10)
Raster Data (14)
Remote Sensing (25)
Data Visualization (4)
Hyperspectral Remote Sensing (18)
Time Series (15)
Phenology (7)
Vector Data (6)
Metadata (1)
Git & GitHub (7)
(1) (1) (14)

Tutorial by R Package

dplyr (7)
ggplot2 (16)
h5py (2)
lubridate (time series) (6)
maps (1)
maptools (1)
plyr (2)
raster (26)
rasterVis (raster time series) (3)
rgdal (GIS) (24)
rgeos (2)
rhdf5 (11)
sp (5)
scales (4)
gridExtra (4)
ggtheme (0)
grid (2)
reshape2 (3)
plotly (5)

View ALL Tutorial Series




Twitter Youtube Github


Blog.Roll

R Bloggers
Date(s): - Aug 6, 2017

Overview

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,
  2. converting timestamps stored as text strings to R date or datetime (e.g. POSIX) classes,
  3. aggregating data across different time scales (day vs month) and
  4. plotting time series data.

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.

TBD: Workshop materials will be posted by July 2017

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.

Download Data

TBD: Workshop materials will be posted by July 2017

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.

#WorkWithData Hashtag

Please tweet using the hashtag #WorkWithData during this workshop!

Workshop Schedule

Location: TBD Please double check the conference schedule as rooms may 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 Workshop Materials will be linked to by July 2017
13:30 ——— BREAK 1 ———
13:45 Workshop Materials will be linked to by July 2017
15:00 ——— BREAK 2 ———
15:15 Workshop Materials will be linked to by July 2017
16:30 Final Questions & Evaluation

Online Tutorials

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


Additional Set Up Resources

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 default to downloading to the Downloads directory on your computer. Note: You may have previously specified a specific directory (folder) for files downloaded from the internet, if so, the .zip file will download there.

3) Move to data directory

Third, move the data files to a directory called data directory within the Documents directory on your computer.

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.


Windows R/RStudio Setup

Once R and R studio are installed, open RStudio to make sure it works and you don’t get any error messages.

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 R studio are installed, open RStudio to make sure it works and you don’t get any error messages.

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 R studio are installed, open RStudio to make sure it works and you don’t get any error messages.