How to Open and Work with NetCDF Data in R

Presented by the ORNL DAAC https://daac.ornl.gov

March 26, 2018

Keywords: R, netCDF

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UPDATE: The entire repo was updated 2022-01-24. This will likely be the last update to the tutorial, as the rgdal package will retire in 2023, and the code would require an extensive rewrite.

1. Overview

In this tutorial we will open some geospatial data that is stored in a netCDF file. Then we will select the variable and time range of interest and export the data as a GeoTIFF file so that we can continue the analysis in R or other geospatial software.

2. Dataset

Long-Term Arctic Growing Season NDVI Trends from GIMMS 3g, 1982-2012

The dataset used in this tutorial provides normalized difference vegetation index (NDVI) data for the Arctic growing season derived primarily with data from Advanced Very High Resolution Radiometer (AVHRR) sensors on board several NOAA satellites over the years 1982 through 2012. The NDVI data, which show vegetation activity, were averaged annually for the arctic growing season (June, July, and August) in each year. The data are circumpolar in coverage at 8-kilometer resolution and limited to greater than 20 degrees North.

Guay, K.C., P.S.A. Beck, and S.J. Goetz. 2015. Long-Term Arctic Growing Season NDVI Trends from GIMMS 3g, 1982-2012. ORNL DAAC, Oak Ridge, Tennessee, USA. https://doi.org/10.3334/ORNLDAAC/1275

Specifically, we will use the file “gimms3g_ndvi_1982-2012.nc4”. With a single click, download the data here https://daac.ornl.gov/daacdata/global_vegetation/GIMMS3g_NDVI_Trends/data/gimms3g_ndvi_1982-2012.nc4 before beginning the tutorial.

3. Prerequisites

Participants should have a basic understanding of R.

3.1 R

1. Download R
2. Download RStudio Recommended
3. Review R Manuals Recommended

4. Procedure

4.1 Tutorial

1. R Markdown
2. Markdown

5. Credits

• R - 4.1.0 (2021-05-18) -- "Camp Pontanezen"
• RStudio - IDE and notebook construction
• ggplot2 - plot figures
• ncdf4 - netcdf manipulation
• raster package - geospatial data manipulations
• rgdal package - bindings for geospatial data manipulations