SoilR (version 1.2.107)

AWBmodel: 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
)

Value

An object of class NlModel that can be further queried.

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).

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))