Nothing
#
# vim:set ff=unix expandtab ts=2 sw=2:
ThreepParallelModel14<-structure(
function #Implementation of a three-pool C14 model with parallel structure
### This function creates a model for two independent (parallel) pools.
### It is a wrapper for the more general function \code{\link{GeneralModel_14}} that can handle an arbitrary number of pools.
(t, ##<< A vector containing the points in time where the solution is sought. It must be specified within the same period for which the Delta 14 C of the atmosphere is provided. The default period in the provided dataset \code{\link{C14Atm_NH}} is 1900-2010.
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.
F0_Delta14C, ##<< A vector of length 3 containing the initial amount of the radiocarbon fraction for the 3 pools in Delta14C values in per mil.
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=1, ##<< A scalar or a data.frame specifying the external (environmental and/or edaphic) effects on decomposition rates.
inputFc,##<< A Data Frame object containing values of atmospheric Delta14C per time. First column must be time values, second column must be Delta14C values in per mil.
lambda=-0.0001209681, ##<< Radioactive decay constant. By default lambda=-0.0001209681 y^-1 . This has the side effect that all your time related data are treated as if the time unit was year.
lag=0, ##<< A positive scalar representing a time lag for radiocarbon to enter the system.
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_stop=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((gam1+gam2)^2 > 1) stop("The sum of the partitioning coefficients gam is outside the interval [0,1]")
if(gam1 < 0 | gam2 < 0) stop("Partitioning coefficients gam must be positive")
if(length(In)==1) inputrates=BoundInFlux(
function(t){matrix(nrow=3,ncol=1,c(gam1*In,gam2*In,(1-gam1-gam2)*In))},
t_start,
t_stop
)
if(class(In)=="data.frame"){
x=In[,1]
y=In[,2]
inputrate=function(t0){as.numeric(spline(x,y,xout=t0)[2])}
inputrates=BoundInFlux(
function(t){matrix(nrow=3,ncol=1,c(gam1*inputrate(t),gam2*inputrate(t),(1-gam1-gam2)*inputrate(t)))},
t_start,
t_stop
)
}
if(length(xi)==1) fX=function(t){xi}
if(class(xi)=="data.frame"){
X=xi[,1]
Y=xi[,2]
fX=function(t){as.numeric(spline(X,Y,xout=t)[2])}
}
At=BoundLinDecompOp(
function(t){
fX(t)*diag(-abs(ks))
},
t_start,
t_stop
)
Fc=BoundFc(inputFc,lag=lag,format="Delta14C")
mod=GeneralModel_14(t,At,ivList=C0,initialValF=ConstFc(F0_Delta14C,"Delta14C"),
inputFluxes=inputrates,Fc,di=lambda,pass=pass)
### A Model Object that can be further queried
##seealso<< \code{\link{TwopSeriesModel14}}, \code{\link{TwopFeedbackModel14}}
}
,
ex=function(){
years=seq(1901,2009,by=0.5)
LitterInput=700
Ex=ThreepParallelModel14(
t=years,
ks=c(k1=1/2.8, k2=1/35, k3=1/100),
C0=c(200,5000,500),
F0_Delta14C=c(0,0,0),
In=LitterInput,
gam1=0.7,
gam2=0.1,
inputFc=C14Atm_NH,
lag=2
)
R14m=getF14R(Ex)
C14m=getF14C(Ex)
C14t=getF14(Ex)
par(mfrow=c(2,1))
plot(C14Atm_NH,type="l",xlab="Year",ylab="Delta 14C (per mil)",xlim=c(1940,2010))
lines(years, C14t[,1], col=4)
lines(years, C14t[,2],col=4,lwd=2)
lines(years, C14t[,3],col=4,lwd=3)
legend(
"topright",
c(
"Delta 14C Atmosphere",
"Delta 14C pool 1",
"Delta 14C pool 2",
"Delta 14C pool 3"
),
lty=rep(1,4),
col=c(1,4,4,4),
lwd=c(1,1,2,3),
bty="n"
)
plot(C14Atm_NH,type="l",xlab="Year",ylab="Delta 14C (per mil)",xlim=c(1940,2010))
lines(years,C14m,col=4)
lines(years,R14m,col=2)
legend("topright",c("Delta 14C Atmosphere","Delta 14C SOM", "Delta 14C Respired"),
lty=c(1,1,1), col=c(1,4,2),bty="n")
par(mfrow=c(1,1))
}
)
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.