bacwaveModel: Implementation of the microbial model Bacwave (bacterial...

In SoilR: Models of Soil Organic Matter Decomposition

Implementation of the microbial model Bacwave (bacterial waves)

Description

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.

Usage

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
)

Arguments

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).

Details

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

Value

An object of class NlModel that can be further queried.

References

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. Microbial Ecology 40: 260-272.

See Also

There are other predefinedModels and also more general functions like Model.

Examples

hours=seq(0,800,0.1)
#
#Run the model with default parameter values
bcmodel=bacwaveModel(t=hours)
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")

SoilR documentation built on Oct. 13, 2023, 5:06 p.m.