R: Implementation of the microbial model AWB (Allison,...

AWBmodel {SoilR}

R Documentation

Implementation of the microbial model AWB (Allison, Wallenstein, Bradford, 2010)

Description

This function implements the microbial model AWB (Allison, Wallenstein, Bradford, 2010), a four-pool model with a microbial biomass, enzyme, SOC and DOC pools. It is a special case of the general nonlinear model.

Usage

AWBmodel(
  t,
  V_M = 1e+08,
  V_m = 1e+08,
  r_B = 2e-04,
  r_E = 5e-06,
  r_L = 0.001,
  a_BS = 0.5,
  epsilon_0 = 0.63,
  epsilon_s = -0.016,
  Km_0 = 500,
  Km_u0 = 0.1,
  Km_s = 0.5,
  Km_us = 0.1,
  Ea = 47,
  R = 0.008314,
  Temp1 = 20,
  Temp2 = 20,
  ival = c(B = 2.19159, E = 0.0109579, S = 111.876, D = 0.00144928),
  I_S = 0.005,
  I_D = 0.005
)

Arguments

`t`	vector of times (in hours) to calculate a solution.
`V_M`	a scalar representing the maximum rate of uptake (mg DOC cm-3 h-1). Equivalent to V_maxuptake0 in original paper.
`V_m`	a scalar representing the maximum rate of decomposition of SOM (mg SOM cm-3 h-1). Equivalent to V_max0 in original paper.
`r_B`	a scalar representing the rate constant of microbial death (h-1). Equivalent to r_death in original publication.
`r_E`	a scalar representing the rate constant of enzyme production (h-1). Equivalent to r_EnzProd in original publication.
`r_L`	a scalar representing the rate constant of enzyme loss (h-1). Equivalent to r_EnzLoss in original publication.
`a_BS`	a scalar representing the fraction of the dead microbial biomass incorporated to SOC. MICtoSOC in original publication.
`epsilon_0`	a scalar representing the intercept of the CUE function (mg mg-1). CUE_0 in original paper.
`epsilon_s`	a scalar representing the slope of the CUE function (degree-1). CUE_slope in original paper.
`Km_0`	a scalar representing the intercept of the half-saturation constant of SOC as a function of temperature (mg cm-3).
`Km_u0`	a scalar representing the intercept of the half saturation constant of uptake as a function of temperature (mg cm-3).
`Km_s`	a scalar representing the slope of the half saturation constant of SOC as a function of temperature (mg cm-3 degree-1).
`Km_us`	a scalar representing the slope of the half saturation constant of uptake as a function of temperature (mg cm-3 degree-1).
`Ea`	a scalar representing the activation energy (kJ mol-1).
`R`	a scalar representing the gas constant (kJ mol-1 degree-1).
`Temp1`	a scalar representing the temperature in the output vector.
`Temp2`	a scalar representing the temperature in the transfer matrix.
`ival`	a vector of length 4 with the initial values for the pools (mg cm-3).
`I_S`	a scalar with the inputs to the SOC pool (mg cm-3 h-1).
`I_D`	a scalar with the inputs to the DOC pool (mg cm-3 h-1).

Details

This implementation contains default parameters presented in Allison et al. (2010).

Value

An object of class NlModel that can be further queried.

References

Allison, S.D., M.D. Wallenstein, M.A. Bradford. 2010. Soil-carbon response to warming dependent on microbial physiology. Nature Geoscience 3: 336-340.

Examples

hours=seq(0,800,0.1)

#Run the model with default parameter values
bcmodel=AWBmodel(t=hours)
Cpools=getC(bcmodel)
##Time solution
# fixme mm:
# the next line causes trouble on Rforge Windows patched build
# matplot(hours,Cpools,type="l",ylab="Concentrations",xlab="Hours",lty=1,ylim=c(0,max(Cpools)*1.2))
##State-space diagram
plot(as.data.frame(Cpools))

[Package SoilR version 1.2.105 Index]