Code Hub
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.
| Title | Description | Tier | Language | |
|---|---|---|---|---|
NEON-AOP-H5toENVIRead AOP HDF5 formatted files from NEON airborne remote sensing surveys in ENVI. Tier 2: NEON certified code ENVI Contributor name:
David Hulslander
License:
BSD 3-clause 'new' or 'revised'
Related collection system:
AOP (Airborne Observation Platform)
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HemiPyA Python module for automated estimation of forest biophysical variables and uncertainties from digital hemispherical photographs. Tier 1: Community contributed code Python For details about HemiPy's algorithms for calculating leaf area index (LAI) and other biophysical metrics from hemispherical photos, see https://doi.org/10.1111/2041-210X.14199 Data products:
DP1.10017.001 | Digital hemispheric photos of plot vegetation
Contributor name:
Courtney Meier
License:
MIT
Related collection system:
TOS (Terrestrial Observation System)
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neonutilitiesAccess NEON data programmatically and stack downloaded files with this handy Python package. Tier 2: NEON certified code Python This package is available to install from PyPi (using pip). It includes functions for accessing and downloading NEON data via the API, including downloading remote sensing data by easting and northing coordinates, and a function to join (stack) the month-by-site files in tabular NEON data. Contributor name:
Claire Lunch
License:
GNU Affero General Public v3.0
Related collection system:
AIS (Aquatic Instrument System), AOP (Airborne Observation Platform), AOS (Aquatic Observation System), SAE (Surface Atmosphere Exchange), TIS (Terrestrial Instrument System), TOS (Terrestrial Observation System)
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PhenofetchPhenofetch is a Command Line Tool/Interface to interact with phenological camera datasets across NEON sites from the Phenocam network. Tier 1: Community contributed code Python Data products:
DP1.00033.001 | Phenology images, DP1.00042.001 | Snow depth and understory phenology images, DP1.20002.001 | Land-water interface images
Contributor name:
Samapriya Roy
License:
Apache 2.0
Related collection system:
AIS (Aquatic Instrument System), TIS (Terrestrial Instrument System)
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DeepForestDeepForest is a Python package for training and predicting ecological objects in airborne imagery. Tier 1: Community contributed code Python DeepForest is a Python package for training and predicting ecological objects in airborne imagery. It was originally developed for tree crown object detection using NEON AOP data and includes a tree detection model trained and evaluated entirely on data from across NEON. The software also provides tools for training and applying multi-class models for applications including species classification. Data products:
DP3.30010.001 | High-resolution orthorectified camera imagery mosaic
Contributor name:
Ethan White
License:
MIT
Related collection system:
AOP (Airborne Observation Platform)
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reaRateThis R package can be used for calculating reaeration rates and associated metrics. Tier 2: NEON certified code R language Contributor name:
Kaelin Cawley
License:
GNU Affero General Public v3.0
Related collection system:
AOS (Aquatic Observation System)
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streamQThis R package calculates stream discharge from slug and constant-rate salt tracer injections. Tier 2: NEON certified code R language Contributor name:
Kaelin Cawley
License:
GNU Affero General Public v3.0
Related collection system:
AOS (Aquatic Observation System)
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stageQCurveCalculates 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 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
Contributor name:
Kaelin Cawley
License:
GNU Affero General Public v3.0
Related collection system:
AIS (Aquatic Instrument System), AOS (Aquatic Observation System)
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eddy4Reddy4R is a family of open-source packages for eddy-covariance (EC) raw data processing, analyses and modeling in the R Language. Tier 3: NEON production code R language As described in Metzger et al. (2017), eddy4R is being developed by NEON scientists with wide input from the scientific community. eddy4R currently consists of the three public packages eddy4R.base, eddy4R.stor, and eddy4R.qaqc, with several additional packages in preparation (including eddy4R.turb, eddy4R.ucrt and eddy4R.erf). Data products:
DP4.00200.001 | Bundled data products - eddy covariance
Contributor name:
Stefan Metzger
License:
GNU Affero General Public v3.0
Related collection system:
TIS (Terrestrial Instrument System)
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neonNtransThis 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 Contributor name:
Samantha Weintraub
License:
GNU Affero General Public v3.0
Related collection system:
TOS (Terrestrial Observation System)
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