14: Implementation of the microbial model Bacwave (bacterial...
In SoilR: Models of Soil Organic Matter Decomposition

Description Usage Arguments Details Value Author(s) References Examples

This function implements the microbial model Bacwave (bacterial waves), a two-pool model with a bacterial and a substrate pool. It is a special case of the general nonlinear model.

1
2
3

bacwaveModel(t, umax = 0.063, ks = 3, theta = 0.23, Dmax = 0.26, 
    kd = 14.5, kr = 0.4, Y = 0.44, ival = c(S0 = 0.5, X0 = 1.5), 
    BGF = 0.15, ExuM = 8, ExuT = 0.8)

`t`	vector of times (in hours) to calculate a solution.
`umax`	a scalar representing the maximum relative growth rate of bacteria (hr-1)
`ks`	a scalar representing the substrate constant for growth (ug C /ml soil solution)
`theta`	a scalar representing soil water content (ml solution/cm3 soil)
`Dmax`	a scalar representing the maximal relative death rate of bacteria (hr-1)
`kd`	a scalar representing the substrate constant for death of bacteria (ug C/ml soil solution)
`kr`	a scalar representing the fraction of death biomass recycling to substrate (unitless)
`Y`	a scalar representing the yield coefficient for bacteria (ug C/ugC)
`ival`	a vector of length 2 with the initial values for the substrate and the bacterial pools (ug C/cm3)
`BGF`	a scalar representing the constant background flux of substrate (ug C/cm3 soil/hr)
`ExuM`	a scalar representing the maximal exudation rate (ug C/(hr cm3 soil))
`ExuT`	a scalar representing the time constant for exudation, responsible for duration of exudation (1/hr).

This implementation containts default parameters presented in Zelenev et al. (2000). It produces nonlinear damped oscillations in the form of a stable focus.

An object of class NlModel that can be further queried.

Carlos A. Sierra, Markus Mueller

Zelenev, V.V., A.H.C. van Bruggen, A.M. Semenov. 2000. “BACWAVE,” a spatial-temporal model for traveling waves of bacterial populations in response to a moving carbon source in soil. Microbail Ecology 40: 260-272.

  hours=seq(0,800,0.1)
  
  #Run the model with default parameter values
  bcmodel=bacwaveModel(t=hours)
# fixme mm:
# the next line causes trouble on Rforge Windows patched build

#  Cpools=getC(bcmodel)
#  
#  #Time solution
#  matplot(hours,Cpools,type="l",ylab="Concentrations",xlab="Hours",lty=1,ylim=c(0,max(Cpools)*1.2))
#  legend("topleft",c("Substrate", "Microbial biomass"),lty=1,col=c(1,2),bty="n")
#  
#  #State-space diagram
#  plot(Cpools[,2],Cpools[,1],type="l",ylab="Substrate",xlab="Microbial biomass")
#  
#  #Microbial biomass over time
#  plot(hours,Cpools[,2],type="l",col=2,xlab="Hours",ylab="Microbial biomass")