Package: neonSoilFlux 1.0.0

neonSoilFlux: Compute Soil Carbon Fluxes for the National Ecological Observatory Network Sites

Acquires and synthesizes soil carbon fluxes at sites located in the National Ecological Observatory Network (NEON). Provides flux estimates and associated uncertainty as well as key environmental measurements (soil water, temperature, CO2 concentration) that are used to compute soil fluxes.

Authors:John Zobitz [aut, cre], Edward Ayres [aut], Katie O'Rourke [ctb], Zoey Werbin [ctb], Lajntxiag Lee [ctb], Ridwan Abdi [ctb], Dijonë Mehmeti [ctb], Ly Xiong [ctb]

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

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

Bug tracker:https://github.com/jmzobitz/neonsoilflux/issues

Datasets:

On CRAN:

Conda-Forge:

5.43 score 6 stars 2 scripts 192 downloads 24 exports 53 dependencies

Last updated 9 months agofrom:0b9cd60878. Checks:5 OK, 3 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 21 2025
R-4.5-winNOTEFeb 21 2025
R-4.5-macNOTEFeb 21 2025
R-4.5-linuxNOTEFeb 21 2025
R-4.4-winOKFeb 21 2025
R-4.4-macOKFeb 21 2025
R-4.3-winOKFeb 21 2025
R-4.3-macOKFeb 21 2025

Exports:acquire_neon_datacheck_qf_flagsco2_to_umolcompute_monthly_meancompute_neon_fluxcompute_surface_fluxcorrect_env_datadejong_shappert_fluxdepth_interpolatedetermine_positiondiffusivityenv_fingerprint_plotfit_functionflux_fingerprint_plothirano_fluxinsert_meaninside_intervalmeasurement_detectmeasurement_mergequadrature_errorswc_correctswc_correctionstang_2003_fluxtang_2005_flux

Dependencies:askpassclicolorspacecpp11curldata.tabledigestdownloaderdplyrfansifarvergenericsggplot2gluegtablehttrisobandjsonlitelabelinglatticelifecyclelubridatemagrittrMASSMatrixmgcvmimemunsellneonUtilitiesnlmeopensslpbapplypillarpkgconfigpurrrR.methodsS3R.ooR.utilsR6RColorBrewerrlangscalesstringistringrsystibbletidyrtidyselecttimechangeutf8vctrsviridisLitewithr

Introducing the neonSoilFlux package

Rendered fromusing-neonSoilFlux.Rmdusingknitr::rmarkdownon Feb 21 2025.

Last update: 2024-05-27
Started: 2024-05-23

Readme and manuals

Help Manual

Help pageTopics
Acquire NEON data for processingacquire_neon_data
Internal helper function to determine availability of data within a time intervalcheck_qf_flags
Convert co2 concentration from ppm to µmol m-3 unitsco2_to_umol
Function to compute monthly means for a given month of NEON data.compute_monthly_mean
Compute NEON fluxes at a sitecompute_neon_flux
Internal fucntion to compute CO2 surface fluxcompute_surface_flux
Internal function that prepares downloaded NEON data for flux processingcorrect_env_data
Internal function to compute surface co2 flux at a given timepoint via De Jong and Schappert (1972)dejong_shappert_flux
Internal function to interpolate different depth measurementsdepth_interpolate
Internal function to determine the depth of a measurementdetermine_position
Compute soil diffusivitydiffusivity
Helper function to plot QF results for environmental measurements.env_fingerprint_plot
Internal function that interpolates a soil measurement to different depthsfit_function
Helper function to plot QF results for fluxes.flux_fingerprint_plot
Internal function to compute surface co2 flux at a given timepoint via Hirano et al 2005hirano_flux
Internal function that inserts smoothed mean value of a measurement at a siteinsert_mean
Determine if a YYYY-MM string is inside a intervalinside_interval
Internal function that makes sure for each time, position, and depth we have at least two data points for soil temp and soil h20, 3 for soil co2measurement_detect
Internal function that filters environmental data for easier processing of fluxes.measurement_merge
Helper function to quickly compute the quadrature errorquadrature_error
Measured environmental data at a NEON sitesjer_env_data_2022_06
Computed flux values at a NEON sitesjer_flux_2022_06
Measured soil physical properties at a NEON sitesjer_megapit_data_2022_06
Internal function to correct depths for VSWC NEON data.swc_correct
Corrected sensor locations for NEON soil water content dataswc_corrections
Internal function to compute surface co2 flux at a given timepoint via Tang et al 2003tang_2003_flux
Internal function to compute surface co2 flux at a given timepoint via Tang et al 2005tang_2005_flux