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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ecocomDPA flexible dataset design pattern for ecological community data to facilitate synthesis and reuse Tier 2: NEON certified code R language This R package provides tools to discover and work with biodiversity data that follow the ecocomDP design pattern, including wrapper functions to search for and download data from the NEON and EDI data portals. See O'Brien et al (2021) for an overview. See the GitHub repo for more information about the data model, tools to work with the data model, and information about planned enhancements and updates. Data products:
DP1.10003.001 | Breeding landbird point counts, DP1.10022.001 | Ground beetles sampled from pitfall traps, DP1.10043.001 | Mosquitoes sampled from CO2 traps, DP1.10058.001 | Plant presence and percent cover, DP1.10072.001 | Small mammal box trapping, DP1.10092.001 | Tick pathogen status, DP1.10093.001 | Ticks sampled using drag cloths, DP1.20107.001 | Fish electrofishing, gill netting, and fyke netting counts, DP1.20120.001 | Macroinvertebrate collection, DP1.20219.001 | Zooplankton collection, DP1.20163.001 | Periphyton, seston, and phytoplankton chemical properties
Contributor name:
Eric Sokol
License:
MIT
Related collection system:
AOS (Aquatic Observation System), TOS (Terrestrial Observation System)
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neonMicrobeThis R package provides functions for working with NEON soil microbe data. Tier 1: Community contributed code R language neonMicrobe is a suite of functions for downloading, pre-processing, and assembling heterogeneous data around the NEON soil microbe marker gene sequence data. To do so, neonMicrobe downloads NEON data products from the NEON Data API and processes sequences using the DADA2 workflow. Qin et al 2021 describes the functionality of this package in detail: https://esajournals.onlinelibrary.wiley.com/doi/full/10.1002/ecs2.3842 Data products:
DP1.10086.001 | Soil physical and chemical properties, periodic, DP1.10108.001 | Soil microbe marker gene sequences
Contributor name:
Clara Qin
License:
GNU General Public v3.0
Related collection system:
TOS (Terrestrial Observation System)
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neonUtilitiesAccess NEON data programmatically and stack downloaded files with this handy R package. Tier 2: NEON certified code R language This package is available to install directly through CRAN. It includes functions for accessing NEON data via the API, a function to join (stack) the month-by-site files in downloaded NEON data, and functions for more specialized data access and conversion, such as extracting flux data from the published HDF5 format and converting data to geoCSV format. Check out our handy cheat sheet! 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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neonOSPerform common transformations on NEON observational data, including table joining and duplicate detection. Tier 2: NEON certified code R language This R package provides functions for standardized duplicate checking and table-joining for NEON observational data products. It uses published metadata from the variables files and Quick Start Guides to determine the correct handling for each data product. neonOS is available via CRAN. Contributor name:
Claire Lunch
License:
GNU Affero General Public v3.0
Related collection system:
AOS (Aquatic Observation System), TOS (Terrestrial Observation System)
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metScanRAccess 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 Contributor name:
Josh Roberti
License:
GNU General Public v3.0
Related collection system:
TIS (Terrestrial Instrument System)
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geoNEONUse 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 Contributor name:
Claire Lunch
License:
GNU Affero General Public v3.0
Related collection system:
AOS (Aquatic Observation System), TOS (Terrestrial Observation System)
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neonDissGasThis 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 Contributor name:
Kaelin Cawley
License:
GNU Affero General Public v3.0
Related collection system:
AOS (Aquatic Observation System)
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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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