Package: NEONiso 0.7.3.9000

Rich Fiorella

NEONiso: Tools to Calibrate and Work with NEON Atmospheric Isotope Data

Functions for downloading, calibrating, and analyzing atmospheric isotope data bundled into the eddy covariance data products of the National Ecological Observatory Network (NEON) <https://www.neonscience.org>. Calibration tools are provided for carbon and water isotope products. Carbon isotope calibration details are found in Fiorella et al. (2021) <doi:10.1029/2020JG005862>, and the readme file at <https://github.com/lanl/NEONiso>. Tools for calibrating water isotope products have been added as of 0.6.0, but have known deficiencies and should be considered experimental and unsupported.

Authors:Rich Fiorella [aut, cre]

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NEONiso.pdf |NEONiso.html✨
NEONiso/json (API)
NEWS

# Install 'NEONiso' in R:
install.packages('NEONiso', repos = c('https://lanl.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lanl/neoniso/issues

Pkgdown site:https://lanl.github.io

On CRAN:

Conda:

5.08 score 2 stars 6 scripts 338 downloads 17 exports 94 dependencies

Last updated 1 months agofrom:f9759b1c31. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 28 2025
R-4.5-winOKMar 28 2025
R-4.5-macOKMar 28 2025
R-4.5-linuxOKMar 28 2025
R-4.4-winOKMar 28 2025
R-4.4-macOKMar 28 2025
R-4.4-linuxOKMar 28 2025
R-4.3-winOKMar 28 2025
R-4.3-macOKMar 28 2025

Exports:calculate_12CO2calculate_13CO2calibrate_ambient_water_linregcalibrate_carbonconvert_NEONhdf5_to_POSIXct_timeconvert_POSIXct_to_NEONhdf5_timecorrect_carbon_ref_cvalcorrect_carbon_ref_outputdelta_to_Rget_Rstdingest_datamanage_local_EC_archiveR_to_deltarestructure_variablesterrestrial_core_sitesterrestrial_gradient_siteswater_isotope_sites

Dependencies:askpasscaretclasscliclockcodetoolscolorspacecpp11curldata.tablediagramdigestdownloaderdplyre1071fansifarverforeachfuturefuture.applygenericsggplot2globalsgluegowergridExtragtablehardhathttripredisobanditeratorsjsonliteKernSmoothlabelinglatticelavalifecyclelistenvlubridatemagrittrMASSMatrixmgcvmimeModelMetricsmunsellneonUtilitiesnlmennetnumDerivopensslparallellypbapplypillarpkgconfigplyrpROCprodlimprogressrproxypurrrR.methodsS3R.ooR.utilsR6RColorBrewerRcpprecipesreshape2rhdf5rhdf5filtersRhdf5librlangrpartscalesshapesparsevctrsSQUAREMstringistringrsurvivalsystibbletidyrtidyselecttimechangetimeDatetzdbutf8vctrsviridisLitewithrzoo

Getting Started with NEONiso

Rendered fromexample_workflow.Rmdusingknitr::rmarkdownon Mar 28 2025.

Last update: 2023-11-27
Started: 2021-02-26

Reference Corrections

Rendered fromreference_corrections.Rmdusingknitr::rmarkdownon Mar 28 2025.

Last update: 2023-07-28
Started: 2022-07-29

Readme and manuals

Help Manual

Help pageTopics
Calculate 12C-CO2 Mole Fractionscalculate_12CO2
Calculate 13C-CO2 Mole Fractionscalculate_13CO2
Calibrate ambient carbon isotope data using gain-and-offset methodcalibrate_ambient_carbon_gainoffset
Calibrate ambient carbon isotope data using linear regressioncalibrate_ambient_carbon_linreg
calibrate_ambient_water_isotopescalibrate_ambient_water_linreg
Calibrate NEON carbon isotope data using validation data sets.calibrate_carbon
Calibrate NEON water isotope ratios using validation data sets.calibrate_water
Make plots of carbon calibration data for debuggingcarbon_regression_plots
Convert NEON HDF5 file time to POSIXctconvert_NEONhdf5_to_POSIXct_time
Convert a POSIXct object to the format used in NEON HDF5 filesconvert_POSIXct_to_NEONhdf5_time
correct_carbon_ref_cvalcorrect_carbon_ref_cval
Correct carbon ref outputcorrect_carbon_ref_output
Converts delta value to heavy-to-light isotope ratiodelta_to_R
Produce estimates of the calibration error.estimate_calibration_error
Extract only the data corresponding to validation/calibration time periods.extract_carbon_cal_data
Extract only the data corresponding to validation/calibration time periods.extract_water_calibration_data
Apply a median absolute deviation filterfilter_median_brock86
Estimate slope/intercept of carbon isotope calibration regressionfit_carbon_regression
Estimate slope/intercept of water isotope calibration regressionfit_water_regression
Return heavy-to-light isotope ratio of primary standard.get_Rstd
Ingest and stack variables needed in calibration.ingest_data
Leave-one-out cross validationloocv
Manage a local eddy covariance (EC) data archive.manage_local_EC_archive
Convert heavy-to-light isotope ratio to delta values.R_to_delta
Restructure ingested variables for the carbon isotope system.restructure_carbon_variables
Restructures data.frames imported by ingest_data to shorten variable names and Wrapper function around restructure_carbon_variables and restructure_water_variables.restructure_variables
Restructure ingested variables for the water isotope system.restructure_water_variables
Select validation data corresponding to a particular dayselect_daily_reference_data
Structure a new HDF5 filesetup_output_file
swap_standard_isotoperatiosswap_standard_isotoperatios
List terrestrial core sitesterrestrial_core_sites
List terrestrial gradient sitesterrestrial_gradient_sites
Standardize analyte namesvalidate_analyte
Validate output file.validate_output_file
List sites with water vapor isotope ratios.water_isotope_sites
Write calibrated carbon ambient data to filewrite_carbon_ambient_data
Write carbon calibrations to filewrite_carbon_calibration_data
Write calibrated ambient water isotope ratio observations to file.write_water_ambient_data
Write water calibration parameters to filewrite_water_calibration_data