# inst/tests/runit.TwopSerial_MCSim.R In SoilR: Models of Soil Organic Matter Decomposition

```#!/usr/bin/Rscript
# vim:set ff=unix expandtab ts=2 sw=2:
test.TwopSerial_MCSim=function(){
# create the operator for a two pool serial model
# according to our new general definition
#
t_start=0
t_end=10
tn=3e2
timestep=(t_end-t_start)/tn
t=seq(t_start,t_end,timestep)
nr=2
# define the transfer functions for the model
# we could compile them to a matrix valued
# Function of C and t since they will be
# applied in a linear way on the output vector.
# but we rather store them in an indexed list
# (as a sparse matrix) which also has some
# implementational benefits because the single
# functions are easier to retrieve from the operator
# if needed.
alpha=list()
#alpha[["2_to_1"]]=function(C,t){
#  1/5#*1e-16
#}
alpha[["1_to_2"]]=function(C,t){
1#all stuff is transmitted
}

k1=3/5
k2=3/5
f=function(C,t){
# in this case the application of f can be expressed by a matrix multiplication
# f(C,t)=N C
# furthermorde the matrix N is actually completely linear and even constant
N=matrix(
nrow=nr,
ncol=nr,
c(
k1,    0,
0  ,  k2
)
)
# so we can write f(C,t)  as a Matrix product
# note however that we could anything we like with the components
# of C here.
# The only thing to take care of is that we release a vector of the same
# size as C
return(N%*%C)
}
fac=2e3

inputrates=new("TimeMap",t_start,t_end,function(t){return(matrix(
nrow=nr,
rep(
c(
2*fac,  0*fac
),
length(t)
)
))})
A=new("TransportDecompositionOperator",t_start,Inf,nr,alpha,f)
mod=GeneralNlModel(
t,
A,
c(
fac,
0
),
inputrates,
deSolve.lsoda.wrapper
)

MCSim=getParticleMonteCarloSimulator(mod)
aPP=availableParticleProperties(MCSim)
aPS=availableParticleSets(MCSim)
ref_PP=c("t_entrySystem","t_entryPool_1","t_entryPool_2","t_exitSystem")
ref_PS=c(
"particles_in_pool_1",
"particles_in_pool_2",
"particles_leaving_pool_1",
"particles_leaving_pool_2",
"particles_leaving_the_system"
)
checkEquals(aPP,ref_PP)
checkEquals(aPS,ref_PS)
mean(
particleSets[["particles_leaving_the_system"]][,"t_exitSystem"]
-particleSets[["particles_leaving_the_system"]][,"t_entrySystem"]
)
)

plot(MCSim)
results=computeResults(MCSim)[["cr"]]
# compare with the ode solutions
Y=getC(mod)
C1sim=results[,"Cstock_1"]
C2sim=results[,"Cstock_2"]
tsim=results[,"time"]
pe(quote(length(tsim)),environment())
pe(quote(length(t)),environment())
#pe(quote(t-tsim),environment())
#checkEquals(t,tsim) # although C1sim had a meaning for t=0 not all the # problems in tasklist have
plot(tsim,C1sim,col="red",ylim=c(min(C1sim,Y[,1],C2sim,Y[,2]),max(C1sim,Y[,1],C2sim,Y[,2])))
points(tsim,C2sim,col="blue")
lines(t,Y[,1],type="l",lty=2,col="red")
lines(t,Y[,2],type="l",lty=2,col="blue")
#check the inputratefunction
ir=getFunctionDefinition(inputrates)
pe(quote(ir(0)),environment())

}
```

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SoilR documentation built on May 29, 2017, 10:57 a.m.