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#' Implementation of a two pool model with series structure
#'
#' This function creates a model for two pools connected in series. It is a
#' wrapper for the more general function \code{\link{GeneralModel}}.
#'
#'
#' @param t A vector containing the points in time where the solution is
#' sought.
#' @param ks A vector of length 2 with the values of the decomposition rate for
#' pools 1 and 2.
#' @param a21 A scalar with the value of the transfer rate from pool 1 to pool
#' 2.
#' @param C0 A vector of length 2 containing the initial amount of carbon for
#' the 2 pools.
#' @param In A scalar or a data.frame object specifying the amount of litter
#' inputs by time.
#' @param xi A scalar or a data.frame specifying the external (environmental
#' and/or edaphic) effects on decomposition rates.
#' @param solver A function that solves the system of ODEs. This can be
#' \code{\link{euler}} or \code{\link{deSolve.lsoda.wrapper}} or any other user
#' provided function with the same interface.
#' @param pass if TRUE Forces the constructor to create the model even if it is
#' invalid
#' @return A Model Object that can be further queried
#' @seealso There are other \code{\link{predefinedModels}} and also more
#' general functions like \code{\link{Model}}.
#' @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)
#' ks=c(k1=0.8,k2=0.4)
#' a21=0.5
#' C0=c(C10=100,C20=150)
#' In = 30
#' #
#' Temp=rnorm(t,15,1)
#' TempEffect=data.frame(t,fT.Daycent1(Temp))
#' #
#' Ex1=TwopSeriesModel(t,ks,a21,C0,In,xi=TempEffect)
#' 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)
#' legend("bottomright",c("Total C","C in pool 1", "C in pool 2"),
#' lty=c(1,1,1),col=c(1,2,4),lwd=c(2,1,1),bty="n")
TwopSeriesModel<- function
(t,
ks,
a21,
C0,
In,
xi=1,
solver=deSolve.lsoda.wrapper,
pass=FALSE
)
{
t_start=min(t)
t_end=max(t)
if(length(ks)!=2) stop("ks must be of length = 2")
if(length(C0)!=2) stop("the vector with initial conditions must be of length = 2")
if(length(In)==1){
inputFluxes=BoundInFluxes(
function(t){matrix(nrow=2,ncol=1,c(In,0))},
t_start,
t_end
)
}
if(inherits(In, "data.frame")){
x=In[,1]
y=In[,2]
inputFlux=splinefun(x,y)
inputFluxes=BoundInFluxes(
function(t){matrix(nrow=2,ncol=1,c(inputFlux(t),0))},
min(x),
max(x)
)
}
A=-1*abs(diag(ks))
A[2,1]=a21
if(length(xi)==1) fX=function(t){xi}
if(inherits(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)
}
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