Package: neonSoilFlux 4.0.0

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]

neonSoilFlux_4.0.0.tar.gz
neonSoilFlux_4.0.0.zip(r-4.7)neonSoilFlux_4.0.0.zip(r-4.6)neonSoilFlux_4.0.0.zip(r-4.5)
neonSoilFlux_4.0.0.tgz(r-4.6-any)neonSoilFlux_4.0.0.tgz(r-4.5-any)
neonSoilFlux_4.0.0.tar.gz(r-4.7-any)neonSoilFlux_4.0.0.tar.gz(r-4.6-any)
neonSoilFlux_4.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
neonSoilFlux/json (API)

# 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:

sjer_env_data_2022_06 - Measured environmental data at a NEON site
sjer_flux_2022_06 - Computed flux values at a NEON site
sjer_megapit_data_2022_06 - Measured soil physical properties at a NEON site

On CRAN:

5.78 score 8 stars 15 scripts 279 downloads 33 exports 57 dependencies

Last updated from:4c33c94322. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	202
source / vignettes	OK	210
linux-release-x86_64	OK	148
macos-release-arm64	OK	98
macos-oldrel-arm64	OK	148
windows-devel	OK	86
windows-release	OK	88
windows-oldrel	OK	92
wasm-release	OK	126

Exports:acquire_neon_data check_qf_flags co2_to_umol compute_flux_gradient_layer compute_monthly_mean compute_neon_flux compute_surface_flux compute_surface_flux_layer correct_env_data dejong_shappert_flux depth_interpolate determine_position diffusivity env_fingerprint_plot fit_function flux_fingerprint_plot get_neon_api_token hirano_flux insert_mean inside_interval linear_regression measurement_detect measurement_merge neon_api_token neonBoulded60Cal neonCal powerset quadrature_error reprocess_vswc swc_correct swc_corrections tang_2003_flux tang_2005_flux

Dependencies:arrow askpass assertthat bit bit64 blob cli cpp11 curl data.table DBI dbplyr digest downloader dplyr duckdb duckdbfs farver fs generics ggplot2 glue gtable httr isoband jose jsonlite labeling lifecycle lubridate magrittr mime neonUtilities openssl pbapply pillar pkgconfig purrr R.methodsS3 R.oo R.utils R6 RColorBrewer rlang S7 scales stringi stringr sys tibble tidyr tidyselect timechange utf8 vctrs viridisLite withr

Using the neonSoilFlux package

Rendered fromusing-neonSoilFlux.Rmdusingknitr::rmarkdown

Last update: 2026-06-29
Started: 2024-05-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Acquire NEON data for processing	acquire_neon_data
Internal helper function to determine availability of data within a time interval	check_qf_flags
Convert co2 concentration from ppm to µmol m-3 units	co2_to_umol
Computes Fick's law of diffusion between two values	compute_flux_gradient_layer
Function to compute monthly means for a given month of NEON data.	compute_monthly_mean
Compute NEON fluxes at a site	compute_neon_flux
Internal function to compute CO2 surface flux	compute_surface_flux
Title Determine the surface flux from linear regression at layers	compute_surface_flux_layer
Internal function that prepares downloaded NEON data for flux processing	correct_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 measurements	depth_interpolate
Internal function to determine the depth of a measurement	determine_position
Compute soil diffusivity	diffusivity
Helper function to plot QF results for environmental measurements.	env_fingerprint_plot
Internal function that interpolates a soil measurement to different depths	fit_function
Helper function to plot QF results for fluxes.	flux_fingerprint_plot
Check to see if a NEON api token is installed	get_neon_api_token
Internal function to compute surface co2 flux at a given timepoint via Hirano et al 2005	hirano_flux
Internal function that inserts smoothed mean value of a measurement at a site	insert_mean
Determine if a YYYY-MM string is inside a interval	inside_interval
Compute linear regression coefficients and errors.	linear_regression
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 co2	measurement_detect
Internal function that filters environmental data for easier processing of fluxes.	measurement_merge
Install a NEON API token in Your '.Renviron' File for repeated Use	neon_api_token
Soil water content calibrations for belowground sensor data	neonBoulded60Cal
Soil water content calibrations for belowground sensor data	neonCal
Compute all possible combinations of a vector - ignoring the empty set	powerset
Helper function to quickly compute the quadrature error	quadrature_error
Internal helper function to reprocess SWC data from calibration data	reprocess_vswc
Measured environmental data at a NEON site	sjer_env_data_2022_06
Computed flux values at a NEON site	sjer_flux_2022_06
Measured soil physical properties at a NEON site	sjer_megapit_data_2022_06
Internal function to correct depths for VSWC NEON data.	swc_correct
Corrected sensor locations for NEON soil water content data	swc_corrections
Internal function to compute surface co2 flux at a given timepoint via Tang et al 2003	tang_2003_flux
Internal function to compute surface co2 flux at a given timepoint via Tang et al 2005	tang_2005_flux