run_PEPRMT — run_PEPRMT • PEPRMT

Wrapper function to run all steps of the PEPRMT model (v1.0).

Usage

run_PEPRMT(
  data,
  wetland_type,
  a0 = 0.7479271,
  a1 = 1.0497113,
  Ha = 149.468171 + 30,
  Hd = 94.4532674 + 100,
  T_opt_GPP = 25 + 274.15,
  Ea_SOM = 18.41329,
  kM_SOM = 1487.65701,
  Ea_labile = 11.65972,
  kM_labile = 61.29611,
  Ea_SOM_CH4 = 14.9025078 + 67.1,
  kM_SOM_CH4 = 0.4644174 + 17,
  Ea_labile_CH4 = 16.7845002 + 71.1,
  kM_labile_CH4 = 0.4359649 + 23,
  Ea_oxi_CH4 = 15.8857612 + 75.4,
  kM_oxi_CH4 = 0.5120464 + 23,
  kI_SO4 = 486.4106939,
  kI_NO3 = 0.1020278,
  k_plant_oxi = 0.35
)

Arguments

data: Data frame containing 15 required columns used as model inputs. See Details for expected column structure.
wetland_type: Integer indicating wetland class: 1 = Freshwater peatland, 2 = Tidal wetland.
a0: Empirical intercept parameter for the fPAR scaling function (unitless). Used in GPP module.
a1: Empirical slope parameter for the fPAR scaling function (unitless). Used in GPP module.
Ha: Activation energy governing the temperature response of photosynthesis for general crop-type vegetation (kJ mol^-1). Controls the rate of increase in GPP with temperature below the thermal optimum. Used in GPP module.
Hd: Deactivation energy controlling the decline in photosynthesis above the thermal optimum (kJ mol^-1). Determines the rate of decrease in GPP at high temperatures. Used in GPP module.
T_opt_GPP: Temperature optimum for GPP. Used in GPP module.
Ea_SOM: – Activation energy controlling the temperature sensitivity of decomposition from the soil organic matter (SOM) pool (kJ mol^-1). Used in Reco module.
kM_SOM: – Half-saturation constant for microbial decomposition of the SOM pool (g C m^-3 soil). Determines substrate limitation strength for SOM respiration. Used in Reco module.
Ea_labile: Activation energy controlling the temperature sensitivity of decomposition from the labile carbon pool (kJ mol^-1). Used in Reco module.
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. Used in Reco module.
Ea_SOM_CH4: Activation energy for methane production from soil organic matter (kJ mol^-1). Used in CH4 module.
kM_SOM_CH4: Half-saturation constant for SOM methane production (g C m^-3 soil). Used in CH4 module.
Ea_labile_CH4: Activation energy for methane production from labile carbon (kJ mol^-1). Used in CH4 module.
kM_labile_CH4: Half-saturation constant for labile methane production (g C m^-3 soil). Used in CH4 module.
Ea_oxi_CH4: Activation energy for methane oxidation (kJ mol^-1). Used in CH4 module.
kM_oxi_CH4: Half-saturation constant for methane oxidation (g C m^-3 soil). Used in CH4 module.
kI_SO4: Sulfate inhibition constant (mg L^-1). Used in CH4 module.
kI_NO3: Nitrate inhibition constant (mg L^-1). Used in CH4 module.
k_plant_oxi: Fraction of CH4 oxidized during transport. Used in CH4 module.

Value

Updated dataframe containing:

GPP: gross primary productivity (g C CO2 m^-2 day^-1)
APAR: absorbed photosynthetically active radiation (umol m-2 d-1)
Reco_full: 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)
pulse_emission_total: total methane emitted (g C CH4 m^-2 day^-1)
Plant_flux_net: net methane flux via plant-mediated transport (g C CH4 m^-2 day^-1)
Hydro_flux: net diffusive methane flux from water to atmosphere (g C CH4 m^-2 day^-1)
M1: methane pool produced from labile soil carbon (g C CH4 m^-3, top meter of soil and water)
M2: methane pool produced from soil organic carbon (g C CH4 m^-3, top meter of soil and water)
trans2: fraction of methane released via plant-mediated transport (unitless)

Details

Runs all PEPRMT functions and returns an output dataframe with modeled GPP, Reco, and CH4

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 with inhibition of methane production in response to salinity and nitrate (Oikawa et al. 2024).

Modules are run sequentially: PEPRMT_GPP, then PEPRMT_Reco, then PEPRMT_CH4.

All variables are expected at a daily time step.

All PEPRMT modules use the same input structure, although not all variables are used in every module.

Required data columns (order does not matter):

DOY: Continuous day of year
DOY_disc: Discontinuous day of year
Year
TA_C: Air temperature (°C)
WTD_cm: Water table depth (cm)
PAR_umol_m2_day: PAR (µmol m^-2 d^-1)
LAI: Leaf Area Index
EVI: Greenness Index
FPAR: FPAR flag
LUE: Light Use Efficiency
Wetland_age_years: Wetland age (years)
Salinity_daily_ave_ppt: Salinity (ppt)
NO3_mg_L: NO3 (mg L^-1)
SOM_MEM_gC_m3: Soil organic matter (g C m^-3)
site: Site identifier