R: Implementation of a three pool model with parallel structure

ThreepParallelModel {SoilR}

R Documentation

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.

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")