Nothing
#
# vim:set ff=unix expandtab ts=2 sw=2:
ThreepSeriesModel<-structure(
function #Implementation of a three pool model with series structure
### This function creates a model for three pools connected in series. It is a wrapper for the more general function \code{\link{GeneralModel}}.
##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.
(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=1, ##<< A scalar or data.frame object specifying the external (environmental and/or edaphic) effects on decomposition rates.
solver=deSolve.lsoda.wrapper, ##<< A function that solves the system of ODEs. This can be \code{\link{euler}} or \code{\link{ode}} or any other user provided function with the same interface.
pass=FALSE ##<< if TRUE Forces the constructor to create the model even if it is invalid
)
{
t_start=min(t)
t_end=max(t)
if(length(ks)!=3) stop("ks must be of length = 3")
if(length(C0)!=3) stop("the vector with initial conditions must be of length = 3")
if(length(In)==1){
inputFluxes=BoundInFlux(
function(t){matrix(nrow=3,ncol=1,c(In,0,0))},
t_start,
t_end
)
}
if(class(In)=="data.frame"){
x=In[,1]
y=In[,2]
inputFlux=splinefun(x,y)
inputFluxes=BoundInFlux(
function(t){matrix(nrow=3,ncol=1,c(inputFlux(t),0,0))},
min(x),
max(x)
)
}
A=-1*abs(diag(ks))
A[2,1]=a21
A[3,2]=a32
if(length(xi)==1) fX=function(t){xi}
if(class(xi)=="data.frame"){
X=xi[,1]
Y=xi[,2]
fX=splinefun(X,Y)
}
Af=BoundLinDecompOp(
function(t){fX(t)*A},
t_start,
t_end
)
Mod=GeneralModel(t=t,A=Af,ivList=C0,inputFluxes=inputFluxes,pass=pass)
return(Mod)
### A Model Object that can be further queried
##seealso<< \code{\link{ThreepParallelModel}}, \code{\link{ThreepFeedbackModel}}
}
,
ex=function(){
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")
}
)
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