Science Score: 67.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: science.org, zenodo.org -
✓Committers with academic emails
2 of 4 committers (50.0%) from academic institutions -
✓Institutional organization owner
Organization lanl has institutional domain (www.lanl.gov) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.9%) to scientific vocabulary
Repository
R package for calibrating NEON atmospheric isotope data
Basic Info
- Host: GitHub
- Owner: lanl
- License: gpl-3.0
- Language: R
- Default Branch: main
- Homepage: https://lanl.github.io/NEONiso/
- Size: 70.2 MB
Statistics
- Stars: 2
- Watchers: 2
- Forks: 2
- Open Issues: 11
- Releases: 14
Metadata Files
README.md
NEONiso
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Author: Rich Fiorella Latest release: February 25, 2025.
This repository contains an R package to calibrate NEON atmospheric isotope data. A stable version of the package can be installed from CRAN, and a development version of this package can be installed here using devtools (see below).
Please report any issues you have, bugs found, or enhancement suggestions as issues to this repository.
Installing the development version:
1) You will need the rhdf5 package, which is not on CRAN. rhdf5 is available from bioconductor using: ```R if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("rhdf5")
2) Install devtools, which is available on CRAN.
3) Install NEONiso from GitHub. Development version can be installed using:
R
devtools::installgithub("lanl/NEONiso")
Alternatively, you can install a specific version of the package (e.g., v0.1)
by specifying the version tag:
R
devtools::installgithub("lanl/NEONiso@v0.1")
```
Citation information:
Package functionality to calibrate NEON carbon isotope data is described in a paper at JGR-Biogeosciences (doi: 10.1029/2020JG005862). Users of this package should also cite the Zenodo DOI above.
Please also check to ensure that you are compliant with NEON's data citation policy for any products derived from this package: https://www.neonscience.org/data/about-data/data-policies
Usage:
Two methods are available to calibrate NEON Carbon isotope data and they take slightly different approaches: a) the 'Bowling2003' method calibrates 12CO2 and 13CO2 mole fractions independently, while b) the 'linreg' method calibrates d13C and CO2 directly without converting to isotopologue mole fractions. The method is specified as an argument to calibratecarbonbymonth(). Both methods yield very similar results, but the error and precision estimates are slightly better from the calibratecarbon_Bowling2003() function (Fiorella et al., 2021; JGR-Biogeosciences)
This function is meant to be applied to a list or vector of uncalibrated data files, and produce output hdf5 files that have (currently) only the CO2 and d13C variables instead of the entire data bundle. Development was targeted and tested on monthly basic files, but the functions should also work on the extended data files.
neonUtilities:::stackEddy should work on these output files - please file an issue if it does not.
DATA ALERT:
Several months of data on the NEON data portal have an issue where the Picarro time clock has diverged from the valve manifold time. A fix has been developed, but has not been propagated to the NEON data portal.
Copyright notice:
© 2022. Triad National Security, LLC. All rights reserved. This program was produced under U.S. Government contract 89233218CNA000001 for Los Alamos National Laboratory (LANL), which is operated by Triad National Security, LLC for the U.S. Department of Energy/National Nuclear Security Administration. All rights in the program are reserved by Triad National Security, LLC, and the U.S. Department of Energy/National Nuclear Security Administration. The Government is granted for itself and others acting on its behalf a nonexclusive, paid-up, irrevocable worldwide license in this material to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so.
Owner
- Name: Los Alamos National Laboratory
- Login: lanl
- Kind: organization
- Email: github-register@lanl.gov
- Location: Los Alamos, New Mexico, USA
- Website: https://www.lanl.gov/
- Repositories: 224
- Profile: https://github.com/lanl
GitHub Events
Total
- Create event: 4
- Release event: 3
- Issues event: 3
- Delete event: 2
- Issue comment event: 1
- Push event: 21
- Pull request event: 2
Last Year
- Create event: 4
- Release event: 3
- Issues event: 3
- Delete event: 2
- Issue comment event: 1
- Push event: 21
- Pull request event: 2
Committers
Last synced: 11 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Rich Fiorella | r****a@u****u | 681 |
| ndurden | n****n@b****g | 49 |
| Hadley Wickham | h****m@g****m | 1 |
| Richard Pascal Fiorella | r****a@p****v | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 57
- Total pull requests: 44
- Average time to close issues: 5 months
- Average time to close pull requests: 2 days
- Total issue authors: 3
- Total pull request authors: 3
- Average comments per issue: 0.79
- Average comments per pull request: 0.64
- Merged pull requests: 43
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 2
- Average time to close issues: 11 days
- Average time to close pull requests: 13 days
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 0.5
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- rfiorella (54)
- jessicaguo (1)
- jmackinnon109 (1)
Pull Request Authors
- rfiorella (39)
- NDurden (4)
- hadley (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- cran 427 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 13
- Total maintainers: 1
cran.r-project.org: NEONiso
Tools to Calibrate and Work with NEON Atmospheric Isotope Data
- Homepage: https://github.com/lanl/NEONiso
- Documentation: http://cran.r-project.org/web/packages/NEONiso/NEONiso.pdf
- License: GPL-3
-
Latest release: 0.7.2
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.0.0 depends
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- ggplot2 * imports
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- lifecycle * imports
- lubridate * imports
- magrittr * imports
- neonUtilities >= 2.0.1 imports
- rhdf5 >= 2.33.7 imports
- rlang * imports
- tidyselect * imports
- zoo * imports
- knitr * suggests
- rmarkdown * suggests
- testthat >= 3.0.0 suggests
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