# Compute Soil Carbon Fluxes for the National Ecological Observatory Network Sites

## Documentation for package ‘neonSoilFlux’ version 4.0.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

acquire_neon_data | Acquire NEON data for processing
check_qf_flags | Internal helper function to determine availability of data within a time interval
co2_to_umol | Convert co2 concentration from ppm to µmol m-3 units
compute_flux_gradient_layer | Computes Fick's law of diffusion between two values
compute_monthly_mean | Function to compute monthly means for a given month of NEON data.
compute_neon_flux | Compute NEON fluxes at a site
compute_surface_flux | Internal function to compute CO2 surface flux
compute_surface_flux_layer | Title Determine the surface flux from linear regression at layers
correct_env_data | Internal function that prepares downloaded NEON data for flux processing
dejong_shappert_flux | Internal function to compute surface co2 flux at a given timepoint via De Jong and Schappert (1972)
depth_interpolate | Internal function to interpolate different depth measurements
determine_position | Internal function to determine the depth of a measurement
diffusivity | Compute soil diffusivity
env_fingerprint_plot | Helper function to plot QF results for environmental measurements.
fit_function | Internal function that interpolates a soil measurement to different depths
flux_fingerprint_plot | Helper function to plot QF results for fluxes.
get_neon_api_token | Check to see if a NEON api token is installed
hirano_flux | Internal function to compute surface co2 flux at a given timepoint via Hirano et al 2005
insert_mean | Internal function that inserts smoothed mean value of a measurement at a site
inside_interval | Determine if a YYYY-MM string is inside a interval
linear_regression | Compute linear regression coefficients and errors.
measurement_detect | 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_merge | Internal function that filters environmental data for easier processing of fluxes.
neonBoulded60Cal | Soil water content calibrations for belowground sensor data
neonCal | Soil water content calibrations for belowground sensor data
neon_api_token | Install a NEON API token in Your '.Renviron' File for repeated Use
powerset | Compute all possible combinations of a vector - ignoring the empty set
quadrature_error | Helper function to quickly compute the quadrature error
reprocess_vswc | Internal helper function to reprocess SWC data from calibration data
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
swc_correct | Internal function to correct depths for VSWC NEON data.
swc_corrections | Corrected sensor locations for NEON soil water content data
tang_2003_flux | Internal function to compute surface co2 flux at a given timepoint via Tang et al 2003
tang_2005_flux | Internal function to compute surface co2 flux at a given timepoint via Tang et al 2005