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Ecosystem Respiration (Reco)

PEPRMT_Reco.Rd

Ecosystem respiration (Reco) module of the PEPRMT model (v1.0).

Usage

PEPRMT_Reco(
  data,
  wetland_type,
  Ea_SOM = 18.41329,
  kM_SOM = 1487.65701,
  Ea_labile = 11.65972,
  kM_labile = 61.29611
)

Arguments

data

Data frame containing 16 required columns used as model inputs. See Details for expected column structure.

wetland_type

Integer indicating wetland class: 1 = Freshwater peatland, 2 = Tidal wetland.

Ea_SOM

– Activation energy controlling the temperature sensitivity of decomposition from the soil organic matter (SOM) pool (kJ mol^-1).

kM_SOM

– Half-saturation constant for microbial decomposition of the SOM pool (g C m^-3 soil). Determines substrate limitation strength for SOM respiration.

Ea_labile

– Activation energy controlling the temperature sensitivity of decomposition from the labile carbon pool (kJ mol^-1).

kM_labile

– Half-saturation constant for microbial decomposition of the labile carbon pool (g C m^-3 soil). Determines substrate limitation strength for labile respiration.

Value

Updated dataframe containing:

Reco_mod

Total ecosystem respiration (g C CO2 m^-2 day^-1)

NEE_mod

Net ecosystem exchange of CO2 (g C CO2 m^-2 day^-1)

S1

Labile soil carbon pool (g C m^-3, top meter of soil)

S2

Soil organic carbon pool (g C m^-3, top meter of soil)

Details

Runs the PEPRMT ecosystem respiration module for freshwater peatlands or tidal wetlands at a daily time step.

The PEPRMT model was originally parameterized for restored freshwater wetlands in the Sacramento–San Joaquin River Delta, California, USA (Oikawa et al. 2017) and later updated for tidal wetlands (Oikawa et al. 2023).

Modules are intended to be run sequentially: PEPRMT_GPP, then PEPRMT_Reco, then PEPRMT_CH4.

All variables are expected at a daily time step.

Required data columns:

  1. Continuous day of year

  2. Discontinuous day of year

  3. Year

  4. Air temperature (°C)

  5. Water table depth (cm)

  6. PAR (µmol m^-2 d^-1)

  7. Leaf Area Index

  8. Greenness Index

  9. FPAR flag

  10. Light Use Efficiency

  11. Wetland age (years)

  12. Salinity (ppt)

  13. NO3 (mg L^-1)

  14. Soil organic matter (g C m^-3)

  15. Site identifier

  16. Modeled GPP (g C m^-2 day^-1)

References

Oikawa, P. Y., Jenerette, G. D., Knox, S. H., Sturtevant, C., Verfaillie, J., Dronova, I., Poindexter, C. M., Eichelmann, E., & Baldocchi, D. D. (2017). Evaluation of a hierarchy of models reveals importance of substrate limitation for predicting carbon dioxide and methane exchange in restored wetlands. Journal of Geophysical Research: Biogeosciences, 122(1), 145–167. https://doi.org/10.1002/2016JG003438

Oikawa, P. Y., Sihi, D., Forbrich, I., Fluet-Chouinard, E., Najarro, M., Thomas, O., Shahan, J., Arias-Ortiz, A., Russell, S., Knox, S. H., McNicol, G., Wolfe, J., Windham-Myers, L., Stuart-Haentjens, E., Bridgham, S. D., Needelman, B., Vargas, R., Schäfer, K., Ward, E. J., Megonigal, P., & Holmquist, J. (2024). A New Coupled Biogeochemical Modeling Approach Provides Accurate Predictions of Methane and Carbon Dioxide Fluxes Across Diverse Tidal Wetlands. Journal of Geophysical Research: Biogeosciences, 129(10), e2023JG007943. https://doi.org/10.1029/2023JG007943

Examples

# Example
# data(example_dataset)
# theta <- c(18.4, 1487.6, 11.6, 61.3)
# out <- PEPRMT_Reco(theta, example_dataset, wetland_type = 2)