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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neonhsWork with NEON hyperspectral data, including extracting spectra from point locations. Tier 1: Community contributed code R language 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.
Data products:
DP3.30006.001 | Spectrometer orthorectified surface directional reflectance - mosaic
Contributor name:
Max Joseph
License:
GNU General Public v3.0
Related collection system:
AOP (Airborne Observation Platform)
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NEON tree crown areaCalculate crown area of woody plants as seen from above based on height and diameter measurements. Tier 1: Community contributed code R language The dataset NEON.DOM.SITE.DP1.10098.001 - Woody plant vegetation structure provides structure measurements, including height, canopy diameter, and stem diameter, as well as mapped position of individual woody plants. However, crowns can overlap and they can also be fully contained within other crowns. In this script, overlapping crown areas are assigned to the taller individual, or split among individuals with the same height. Crown areas of smaller individuals completely covered by taller individuals are omitted. Data products:
DP1.10098.001 | Vegetation structure
Contributor name:
Anna Schweiger
License:
MIT
Related collection system:
AOP (Airborne Observation Platform), TOS (Terrestrial Observation System)
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neonPlantEcologyReformat and process plant presence and percent cover data Tier 1: Community contributed code R language This package contains scripts for processing plant species cover and occurrence data from NEON into more usable formats. The main functions are 'vegify', which creates vegan-friendly species occurrence and abundance matrices, and 'get_diversity_info', which creates summary statistics by plot (or subplot) on the diversity, cover, relative cover, and number of species of natives, non-natives, and members of the family or species of your choosing. Data products:
DP1.10058.001 | Plant presence and percent cover
Contributor name:
Adam Mahood
License:
MIT
Related collection system:
TOS (Terrestrial Observation System)
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neonstoreThis package provides a high-level interface for downloading and storing NEON data products. Tier 1: Community contributed code R language Provides functions for downloading and storing NEON data files. By using persistent storage, this package avoids repeated downloading of the same data, but enables retention of older versions of data that have since been updated. This storage system facilitates reproducibility. Also includes an option to construct a local duckdb database to work with tables that are too large to store in memory. Contributor name:
Carl Boettiger
License:
MIT
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NEONisoThis R package provides functions for downloading and calibrating atmospheric isotope data bundled into the eddy covariance data products. Tier 1: Community contributed code R language This R package provides functions for downloading and calibrating atmospheric isotope data bundled into the eddy covariance data products. The carbon isotope calibration methods are described in Fiorella et al. (2021; JGR-Biogeosciences) and are available in the CRAN version of the package, while water isotope calibration methods remain in development on Github. Data products:
DP1.00036.001 | Atmospheric CO2 isotopes, DP1.00037.001 | Atmospheric H2O isotopes, DP4.00200.001 | Bundled data products - eddy covariance
Contributor name:
Rich Fiorella
Related collection system:
SAE (Surface Atmosphere Exchange), TIS (Terrestrial Instrument System)
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