ThreepParallelModel: Implementation of a three pool model with parallel structure

In SoilR: Models of Soil Organic Matter Decomposition

Implementation of a three pool model with parallel structure

Description

The function creates a model for three independent (parallel) pools. It is a wrapper for the more general function ParallelModel that can handle an arbitrary number of pools.

Usage

ThreepParallelModel(
  t,
  ks,
  C0,
  In,
  gam1,
  gam2,
  xi = 1,
  solver = deSolve.lsoda.wrapper,
  pass = FALSE
)

Arguments

t	A vector containing the points in time where the solution is sought.
ks	A vector of length 3 containing the decomposition rates for the 3 pools.
C0	A vector of length 3 containing the initial amount of carbon for the 3 pools.
In	A scalar or a data.frame object specifying the amount of litter inputs by time.
gam1	A scalar representing the partitioning coefficient, i.e. the proportion from the total amount of inputs that goes to pool 1.
gam2	A scalar representing the partitioning coefficient, i.e. the proportion from the total amount of inputs that goes to pool 2.
xi	A scalar or a data.frame specifying the external (environmental and/or edaphic) effects on decomposition rates.
solver	A function that solves the system of ODEs. This can be euler or deSolve.lsoda.wrapper or any other user provided function with the same interface.
pass	Logical that forces the Model to be created even if the chect suggest problems.

References

Sierra, C.A., M. Mueller, S.E. Trumbore. 2012. Models of soil organic matter decomposition: the SoilR package version 1.0. Geoscientific Model Development 5, 1045-1060.

See Also

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

Examples

t_start=0 
t_end=10 
tn=50
timestep=(t_end-t_start)/tn 
t=seq(t_start,t_end,timestep) 

Ex=ThreepParallelModel(t,ks=c(k1=0.5,k2=0.2,k3=0.1),
C0=c(c10=100, c20=150,c30=50),In=20,gam1=0.7,gam2=0.1,xi=0.5)
Ct=getC(Ex)

plot(t,rowSums(Ct),type="l",lwd=2,
ylab="Carbon stocks (arbitrary units)",xlab="Time",ylim=c(0,sum(Ct[1,]))) 
lines(t,Ct[,1],col=2)
lines(t,Ct[,2],col=4)
lines(t,Ct[,3],col=3)
legend("topright",c("Total C","C in pool 1", "C in pool 2","C in pool 3"),
lty=c(1,1,1,1),col=c(1,2,4,3),lwd=c(2,1,1,1),bty="n")

Rt=getReleaseFlux(Ex)
plot(t,rowSums(Rt),type="l",ylab="Carbon released (arbitrary units)",
xlab="Time",lwd=2,ylim=c(0,sum(Rt[1,]))) 
lines(t,Rt[,1],col=2)
lines(t,Rt[,2],col=4)
lines(t,Rt[,3],col=3)
legend("topright",c("Total C release","C release from pool 1",
"C release from pool 2","C release from pool 3"),
lty=c(1,1,1,1),col=c(1,2,4,3),lwd=c(2,1,1,1),bty="n")

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