205: Implementation of a three pool model with series structure

In SoilR: Models of Soil Organic Matter Decomposition

Description

This function creates a model for three pools connected in series. It is a wrapper for the more general function GeneralModel.

Usage

ThreepSeriesModel(t, ks, a21, a32, C0, In, 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 lenght 3 containing the values of the decomposition rates for pools 1, 2, and 3.
a21	A scalar with the value of the transfer rate from pool 1 to pool 2.
a32	A scalar with the value of the transfer rate from pool 2 to pool 3.
C0	A vector of length 3 containing the initial amount of carbon for the 3 pools.
In	A scalar or data.frame object specifying the amount of litter inputs by time.
xi	A scalar or data.frame object 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 ode or any other user provided function with the same interface.
pass	if TRUE Forces the constructor to create the model even if it is invalid

Value

A Model Object that can be further queried

Author(s)

Carlos A. Sierra, Markus Mueller

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

ThreepParallelModel, ThreepFeedbackModel

Examples

t_start=0 
t_end=10 
tn=50
timestep=(t_end-t_start)/tn 
t=seq(t_start,t_end,timestep) 
ks=c(k1=0.8,k2=0.4,k3=0.2)
C0=c(C10=100,C20=150, C30=50)
In = 50

Ex1=ThreepSeriesModel(t=t,ks=ks,a21=0.5,a32=0.2,C0=C0,In=In,xi=fT.Q10(15))
Ct=getC(Ex1)
Rt=getReleaseFlux(Ex1)

plot(t,rowSums(Ct),type="l",ylab="Carbon stocks (arbitrary units)",
     xlab="Time (arbitrary units)",lwd=2,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")

plot(t,rowSums(Rt),type="l",ylab="Carbon released (arbitrary units)",
     xlab="Time (arbitrary units)",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")

Inr=data.frame(t,Random.inputs=rnorm(length(t),50,10))
plot(Inr,type="l")

Ex2=ThreepSeriesModel(t=t,ks=ks,a21=0.5,a32=0.2,C0=C0,In=Inr)
Ctr=getC(Ex2)
Rtr=getReleaseFlux(Ex2)

plot(t,rowSums(Ctr),type="l",ylab="Carbon stocks (arbitrary units)",
     xlab="Time (arbitrary units)",lwd=2,ylim=c(0,sum(Ctr[1,]))) 
lines(t,Ctr[,1],col=2)
lines(t,Ctr[,2],col=4)
lines(t,Ctr[,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")

plot(t,rowSums(Rtr),type="l",ylab="Carbon released (arbitrary units)",
     xlab="Time (arbitrary units)",lwd=2,ylim=c(0,sum(Rtr[1,]))) 
lines(t,Rtr[,1],col=2)
lines(t,Rtr[,2],col=4)
lines(t,Rtr[,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 May 4, 2017, 9:08 p.m.