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  1. Resources
  2. Code Hub

Code Hub

Workshop banner with code

NEON's data are often complex; working with data can be greatly simplified using software or code. We provide some code to get you started, like with our `neonUtilities` package for R, and also post links to code contributed by members of the community. The NEON-related code resources listed below are designed to make working with all NEON data easier, to perform common algorithms on select data products, and to share the code used to generate select  data products.

Most code resources that were created by and are managed by NEON can be found in the NEONScience GitHub organization. The code is free and open access to download and utilize. The code found in the NEONScience GitHub organization is published and maintained by NEON project scientists. 

Other code resources listed below are created by data users interested in sharing their code. If you have requests for coding resources, challenges with NEON data or ideas for creating NEON data-related code, we encourage you to learn more about how we categorize NEON-related code resources, and how you can submit your own code resources.

Code resources are provided at three tiers, differing in level of review by NEON:

Tier 1: Community Contributed Code Community contributed code is reviewed to determine that it is publicly available, generally comprehensible, and involves NEON data. Code functionality is not evaluated.
Tier 2: NEON Certified Code Certified code goes through a code review, to ensure it performs as described and without error.
Tier 3: NEON Production Code Production code is used in NEON data processing pipelines, to generate NEON data products. It is the end product of a very long and careful development process.

Search the table below to find code that might be useful for your project.

Language
    Title
  • Description
  • Tier
  • Language

NEON-AOP-H5toENVI

Read AOP HDF5 formatted files from NEON airborne remote sensing surveys in ENVI.

Tier 2: NEON certified code
ENVI
More Details
More Info
Tier:
Tier 2: NEON certified code
Coding Language:
ENVI
Contributor name:
David Hulslander
License:
BSD 3-clause 'new' or 'revised'
Related collection system:
AOP (Airborne Observation Platform)

metScanR

Access meteorological data from a growing database that contains metadata for >100,000 stations from 219 countries or territories worldwide — including all NEON sites.

Tier 2: NEON certified code
R language
More Details
More Info
Tier:
Tier 2: NEON certified code
Coding Language:
R language
Contributor name:
Josh Roberti
License:
GNU General Public v3.0
Related collection system:
TIS (Terrestrial Instrument System)

geoNEON

Use R to handle NEON geolocation data, including extracting spatial data from the API based on a named location, and calculating more precise locations for select observational data products.

Tier 2: NEON certified code
R language
More Details
More Info
Tier:
Tier 2: NEON certified code
Coding Language:
R language
Contributor name:
Claire Lunch
License:
GNU Affero General Public v3.0
Related collection system:
AOS (Aquatic Observation System), TOS (Terrestrial Observation System)

neonDissGas

This R package is for calculating dissolved gas concentrations in surface water samples from reference air and water equilibrated gas samples.

Tier 2: NEON certified code
R language
More Details
More Info
Data products:
DP1.20097.001 | Dissolved gases in surface water
Tier:
Tier 2: NEON certified code
Coding Language:
R language
Contributor name:
Kaelin Cawley
License:
GNU Affero General Public v3.0
Related collection system:
AOS (Aquatic Observation System)

reaRate

This R package can be used for calculating reaeration rates and associated metrics.

Tier 2: NEON certified code
R language
More Details
More Info
Data products:
DP1.20190.001 | Reaeration field and lab collection
Tier:
Tier 2: NEON certified code
Coding Language:
R language
Contributor name:
Kaelin Cawley
License:
GNU Affero General Public v3.0
Related collection system:
AOS (Aquatic Observation System)

streamQ

This R package calculates stream discharge from slug and constant-rate salt tracer injections.

Tier 2: NEON certified code
R language
More Details
More Info
Data products:
DP1.20193.001 | Salt-based stream discharge
Tier:
Tier 2: NEON certified code
Coding Language:
R language
Contributor name:
Kaelin Cawley
License:
GNU Affero General Public v3.0
Related collection system:
AOS (Aquatic Observation System)

stageQCurve

Calculates the Stage-Discharge Rating Curve for a Site and Water Year and creates a continuous discharge record from water level data.

Tier 3: NEON production code
R language
More Details
More Info
Data products:
DP1.20048.001 | Discharge field collection, DP1.20267.001 | Gauge height, DP4.00130.001 | Continuous discharge, DP4.00133.001 | Stage-discharge rating curves
Tier:
Tier 3: NEON production code
Coding Language:
R language
Contributor name:
Kaelin Cawley
License:
GNU Affero General Public v3.0
Related collection system:
AIS (Aquatic Instrument System), AOS (Aquatic Observation System)

neonNtrans

This R package is for calculating soil extractable inorganic nitrogen (N) concentrations and net N transformation rates (mineralization and nitrification) from soil potassium chloride extracts.

Tier 2: NEON certified code
R language
More Details
More Info
Data products:
DP1.10080.001 | Soil inorganic nitrogen pools and transformations
Tier:
Tier 2: NEON certified code
Coding Language:
R language
Contributor name:
Samantha Weintraub
License:
GNU Affero General Public v3.0
Related collection system:
TOS (Terrestrial Observation System)

neonhs

Work with NEON hyperspectral data, including extracting spectra from point locations.

Tier 1: Community contributed code
R language
More Details

The goal of neonhs is to make data from the National Ecological Observatory Network (NEON) Airborne Observation Platform (AOP) hyperspectral instrument easier to use. It allows you to efficiently extract spectra from spatial point locations, without worrying about the details of how the hyperspectral data are structured and stored.

 

More Info
Data products:
DP3.30006.001 | Spectrometer orthorectified surface directional reflectance - mosaic
Tier:
Tier 1: Community contributed code
Coding Language:
R language
Contributor name:
Max Joseph
License:
GNU General Public v3.0
Related collection system:
AOP (Airborne Observation Platform)

Phenocam & Repeat Photography

The PhenoCam Network develops and hosts a variety of tools to work with phenocam and other repeat photography images. Tools have been developed in R, Python and interactive GUIs.

Tier 2: NEON certified code
More Details

The tools include: 

  • phenocamapi R package: Access and work with NEON phenocam data (phenology images,  DP1.00033.001; land-water interface images, DP1.20002.001; snow depth and understory phenology images, DP1.00042.001) from the Phenocam Network directly to your R workspace or computer.
  • xROI R package: Delineate Region of Interests (ROI's) and extract time series data from the image. 
  • phenocamr and phenor R packages: Provide phenology modelling tools. 
More Info
Data products:
DP1.00033.001 | Phenology images, DP1.00042.001 | Snow depth and understory phenology images, DP1.20002.001 | Land-water interface images
Tier:
Tier 2: NEON certified code
Contributor name:
Phenocam
License:
GNU Affero General Public v3.0
Related collection system:
AIS (Aquatic Instrument System), TIS (Terrestrial Instrument System)

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The National Ecological Observatory Network is a major facility fully funded by the National Science Foundation.

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