Learn R Programming

neonSoilFlux

neonSoilFlux is a repository code to acquire, tidy, and compute soil respiration fluxes at NEON sites using the flux-gradient method.

An online applet for visualization at select NEON sites is found here

Installation

Installation in R through:

  • CRAN: install.packages(neonSoilFlux)
  • Github using the devtools package:

devtools::install_github("jmzobitz/neonSoilFlux", build = TRUE, build_opts = c("--no-resave-data", "--no-manual"),force=TRUE)

If you encounter problems with code in this repository, feel free to post an issue.

Usage

To analyze fluxes once the package is installed requires a two step process:

  1. Load up the tidyverse and lubridate libraries (library(tidyverse) and library(lubridate). We are heavily making use of dplyr and purrr, so this should get you covered.

  2. First acquire the NEON data, following conventions of loadByProduct function in the neonUtilities package.

out_env_data <- acquire_neon_data(site_name = 'SJER', download_date = '2021-06', )

  1. Then process and compute fluxes.

out_fluxes <- compute_neon_flux(input_site_env = out_env_data$site_data, input_site_megapit = out_env_data$site_megapit )

You now have a data frame of computed fluxes.

More detailed usage information is given in the vignette using-neonSoilFlux (vignette(using-neonSoilFlux)).

Credits & Acknowledgements

The package neonSoilFlux was funded with support from the National Science Foundation, grant #2017829. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

The National Ecological Observatory Network is a program sponsored by the National Science Foundation and operated under cooperative agreement by Battelle. This material is based in part upon work supported by the National Science Foundation through the NEON Program.

Code Contributions / Changelog:

  • (pre-2021): Initial code developed by Edward Ayres (eayres@battelleecology.org)
  • 2021: Initial package development and testing by Zobitz and undergraduate researchers Lajntxiag Lee and Kathleen O'Rourke (both Augsburg University)
  • 2022: Ongoing refinement and testing by undergraduate researchers at the following institutions:
    • Ridwan Abdi, Kebba Janeh, Nevin Lor, Diana Ortiz Alvarracin, Dijone Mehmeti, Ali Musa, Barbara Sabino Pina, Ly Xiong, Xeng Yang (Augsburg University)
    • Courtney Leung (Northwestern University)
  • 2024: Refinement to include a gapfilling routine from Zoey Werbin at Boston University as well as additional calculations of the soil flux via different approaches in Maier, M., and H. Schack-Kirchner. 2014. “Using the Gradient Method to Determine Soil Gas Flux: A Review.” Agricultural and Forest Meteorology 192–193 (July): 78–95. https://doi.org/10.1016/j.agrformet.2014.03.006.
  • 05.2024 Renaming of pacakge to neonSoilFlux from NEONSoils and associated updates to prepare for CRAN submission.

License

GNU Affero General Public License Version 3, 19 November 2007

Disclaimer

Information and documents contained within this repository are available as-is. Codes or documents, or their use, may not be supported or maintained under any program or service and may not be compatible with data currently available from the NEON Data Portal.

Copy Link

Version

Install

install.packages('neonSoilFlux')

Monthly Downloads

166

Version

1.0.0

License

GPL (>= 3)

Issues

3

Pull Requests

0

Stars

8

Forks

8

Maintainer

John Zobitz

Last Published

May 25th, 2024

Functions in neonSoilFlux (1.0.0)

swc_correct

Internal function to correct depths for VSWC NEON data.
flux_fingerprint_plot

Helper function to plot QF results for fluxes.
swc_corrections

Corrected sensor locations for NEON soil water content data
fit_function

Internal function that interpolates a soil measurement to different depths
hirano_flux

Internal function to compute surface co2 flux at a given timepoint via Hirano et al 2005
sjer_megapit_data_2022_06

Measured soil physical properties at a NEON site
quadrature_error

Helper function to quickly compute the quadrature error
sjer_flux_2022_06

Computed flux values at a NEON site
sjer_env_data_2022_06

Measured environmental data at a NEON site
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
insert_mean

Internal function that inserts smoothed mean value of a measurement at a site
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
env_fingerprint_plot

Helper function to plot QF results for environmental measurements.
diffusivity

Compute soil diffusivity
depth_interpolate

Internal function to interpolate different depth measurements
determine_position

Internal function to determine the depth of a measurement
co2_to_umol

Convert co2 concentration from ppm to µmol m-3 units
compute_monthly_mean

Function to compute monthly means for a given month of NEON data.
correct_env_data

Internal function that prepares downloaded NEON data for flux processing
acquire_neon_data

Acquire NEON data for processing
dejong_shappert_flux

Internal function to compute surface co2 flux at a given timepoint via De Jong and Schappert (1972)
compute_surface_flux

Internal fucntion to compute CO2 surface flux
compute_neon_flux

Compute NEON fluxes at a site
check_qf_flags

Internal helper function to determine availability of data within a time interval
measurement_merge

Internal function that filters environmental data for easier processing of fluxes.
inside_interval

Determine if a YYYY-MM string is inside a interval
neonSoilFlux-package

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