| ThreepFeedbackModel14 {SoilR} | R Documentation |
This function creates a model for three pools connected with feedback. It
is a wrapper for the more general function GeneralModel_14
that can handle an arbitrary number of pools with arbitrary connections.
GeneralModel_14 can also handle input data in different
formats, while this function requires its input as Delta14C. Look at it as
an example how to use the more powerful tool GeneralModel_14
or as a shortcut for a standard task!
ThreepFeedbackModel14( t, ks, C0, F0_Delta14C, In, a21, a12, a32, a23, xi = 1, inputFc, lambda = -0.0001209681, lag = 0, solver = deSolve.lsoda.wrapper, pass = FALSE )
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
|
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 fraction of radiocarbon for the 3 pools in Delta14C format. The format will be assumed to be Delta14C, so please take care that it is. |
In |
A scalar or a data.frame object specifying the amount of litter inputs by time. |
a21 |
A scalar with the value of the transfer rate from pool 1 to pool 2. |
a12 |
A scalar with the value of the transfer rate from pool 2 to pool 1. |
a32 |
A scalar with the value of the transfer rate from pool 2 to pool 3. |
a23 |
A scalar with the value of the transfer rate from pool 3 to pool 2. |
xi |
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 |
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 |
A positive scalar representing a time lag for radiocarbon to enter the system. |
solver |
A function that solves the system of ODEs. This can be
|
pass |
if TRUE forces the constructor to create the model even if it is invalid. This is sometimes useful when SoilR is used by external packages for parameter estimation. |
There are other predefinedModels and also more
general functions like Model_14.
#years=seq(1901,2009,by=0.5)
years=seq(1904,2009,by=0.5)
LitterInput=100
k1=1/2; k2=1/10; k3=1/50
a21=0.9*k1
a12=0.4*k2
a32=0.4*k2
a23=0.7*k3
Feedback=ThreepFeedbackModel14(
t=years,
ks=c(k1=k1, k2=k2, k3=k3),
C0=c(100,500,1000),
F0_Delta14C=c(0,0,0),
In=LitterInput,
a21=a21,
a12=a12,
a32=a32,
a23=a23,
inputFc=C14Atm_NH
)
F.R14m=getF14R(Feedback)
F.C14m=getF14C(Feedback)
F.C14t=getF14(Feedback)
Series=ThreepSeriesModel14(
t=years,
ks=c(k1=k1, k2=k2, k3=k3),
C0=c(100,500,1000),
F0_Delta14C=c(0,0,0),
In=LitterInput,
a21=a21,
a32=a32,
inputFc=C14Atm_NH
)
S.R14m=getF14R(Series)
S.C14m=getF14C(Series)
S.C14t=getF14(Series)
Parallel=ThreepParallelModel14(
t=years,
ks=c(k1=k1, k2=k2, k3=k3),
C0=c(100,500,1000),
F0_Delta14C=c(0,0,0),
In=LitterInput,
gam1=0.6,
gam2=0.2,
inputFc=C14Atm_NH,
lag=2
)
P.R14m=getF14R(Parallel)
P.C14m=getF14C(Parallel)
P.C14t=getF14(Parallel)
par(mfrow=c(3,2))
plot(
C14Atm_NH,
type="l",
xlab="Year",
ylab=expression(paste(Delta^14,"C ","(\u2030)")),
xlim=c(1940,2010)
)
lines(years, P.C14t[,1], col=4)
lines(years, P.C14t[,2],col=4,lwd=2)
lines(years, P.C14t[,3],col=4,lwd=3)
legend(
"topright",
c("Atmosphere", "Pool 1", "Pool 2", "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=expression(paste(Delta^14,"C ","(\u2030)")),xlim=c(1940,2010))
lines(years,P.C14m,col=4)
lines(years,P.R14m,col=2)
legend("topright",c("Atmosphere","Bulk SOM", "Respired C"),
lty=c(1,1,1), col=c(1,4,2),bty="n")
plot(C14Atm_NH,type="l",xlab="Year",
ylab=expression(paste(Delta^14,"C ","(\u2030)")),xlim=c(1940,2010))
lines(years, S.C14t[,1], col=4)
lines(years, S.C14t[,2],col=4,lwd=2)
lines(years, S.C14t[,3],col=4,lwd=3)
legend("topright",c("Atmosphere", "Pool 1", "Pool 2", "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=expression(paste(Delta^14,"C ","(\u2030)")),xlim=c(1940,2010))
lines(years,S.C14m,col=4)
lines(years,S.R14m,col=2)
legend("topright",c("Atmosphere","Bulk SOM", "Respired C"),
lty=c(1,1,1), col=c(1,4,2),bty="n")
plot(C14Atm_NH,type="l",xlab="Year",
ylab=expression(paste(Delta^14,"C ","(\u2030)")),xlim=c(1940,2010))
lines(years, F.C14t[,1], col=4)
lines(years, F.C14t[,2],col=4,lwd=2)
lines(years, F.C14t[,3],col=4,lwd=3)
legend("topright",c("Atmosphere", "Pool 1", "Pool 2", "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=expression(paste(Delta^14,"C ","(\u2030)")),xlim=c(1940,2010))
lines(years,F.C14m,col=4)
lines(years,F.R14m,col=2)
legend("topright",c("Atmosphere","Bulk SOM", "Respired C"),
lty=c(1,1,1), col=c(1,4,2),bty="n")
par(mfrow=c(1,1))