# inst/tests/automatic/runit.FourpSerial_1.R In SoilR: Models of Soil Organic Matter Decomposition

```# This test function is automatically produced by the python script:/home/mm/SoilR/RPackages/SoilR/pkg/inst/tests/automatic/Rexample.py
test.FourpSerial_1=function(){
require(RUnit)
t_start=0
t_end=2
tn=100
tol=.02/tn
print(tol)
timestep=(t_end-t_start)/tn
t=seq(t_start,t_end,timestep)
A=new("ConstLinDecompOp",matrix(
nrow=4,
ncol=4,
c(
-1,  1,  0,  0,
0,  -2,  1,  1,
0,  0,  -2,  1,
0,  0,  1,  -1
)
))
c01=3
c02=2
c03=1
c04=0
inputrates=new("TimeMap",t_start,t_end,function(t){return(matrix(
nrow=4,
ncol=1,
c(
1,  2,  3,  4
)
))})
Y=matrix(ncol=4,nrow=length(t))
Y[,1]=c01*exp(-t) + 1 - exp(-t)
Y[,2]=c01*(exp(-t) - exp(-2*t)) + c02*exp(-2*t) + 3/2 - exp(-t) - exp(-2*t)/2
Y[,3]=c01*(-2*(1/(-sqrt(5)/2 - 1/2) - 2/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) + 4*(-1/(2*(-sqrt(5)/2 - 1/2)) + 1)/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)))*exp(t*(-3/2 - sqrt(5)/2))/(-1 + sqrt(5)) - 2*(-1/(-sqrt(5)/2 + 5/2) + 2*(-1/(2*(-sqrt(5)/2 - 1/2)) + 1)/(-sqrt(5)/2 + 5/2))*exp(t*(-3/2 + sqrt(5)/2))/(-sqrt(5) - 1) - exp(-t)) + c02*(-4*exp(t*(-3/2 - sqrt(5)/2))/((-1 + sqrt(5))*(-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) - 2*exp(t*(-3/2 + sqrt(5)/2))/((-sqrt(5) - 1)*(-sqrt(5)/2 + 5/2))) + c03*(-2*(1/(-sqrt(5)/2 - 1/2) - 2/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)**2*(-sqrt(5)/2 + 5/2)))*exp(t*(-3/2 - sqrt(5)/2))/(-1 + sqrt(5)) + 2*exp(t*(-3/2 + sqrt(5)/2))/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2))) + c04*(-4*exp(t*(-3/2 - sqrt(5)/2))/((-1 + sqrt(5))*(-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) - 2*exp(t*(-3/2 + sqrt(5)/2))/((-sqrt(5) - 1)*(-sqrt(5)/2 + 5/2))) - 24*(-3*exp(-3*t/2)*exp(-sqrt(5)*t/2)/2 + sqrt(5)*exp(-3*t/2)*exp(-sqrt(5)*t/2)/2)/((-1 + sqrt(5))*(-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) - 2*(-3*exp(-3*t/2)*exp(-sqrt(5)*t/2)/2 + sqrt(5)*exp(-3*t/2)*exp(-sqrt(5)*t/2)/2)*(1/(-sqrt(5)/2 - 1/2) - 2/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) + 4*(-1/(2*(-sqrt(5)/2 - 1/2)) + 1)/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)))/(-1 + sqrt(5)) - 6*(-3*exp(-3*t/2)*exp(-sqrt(5)*t/2)/2 + sqrt(5)*exp(-3*t/2)*exp(-sqrt(5)*t/2)/2)*(1/(-sqrt(5)/2 - 1/2) - 2/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)**2*(-sqrt(5)/2 + 5/2)))/(-1 + sqrt(5)) - 2*(-3*exp(-3*t/2)*exp(sqrt(5)*t/2)/2 - sqrt(5)*exp(-3*t/2)*exp(sqrt(5)*t/2)/2)*(-1/(-sqrt(5)/2 + 5/2) + 2*(-1/(2*(-sqrt(5)/2 - 1/2)) + 1)/(-sqrt(5)/2 + 5/2))/(-sqrt(5) - 1) + 6*(-3*exp(-3*t/2)*exp(sqrt(5)*t/2)/2 - sqrt(5)*exp(-3*t/2)*exp(sqrt(5)*t/2)/2)/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) - 12*(-3*exp(-3*t/2)*exp(sqrt(5)*t/2)/2 - sqrt(5)*exp(-3*t/2)*exp(sqrt(5)*t/2)/2)/((-sqrt(5) - 1)*(-sqrt(5)/2 + 5/2)) + 24*(-3/2 + sqrt(5)/2)/((-1 + sqrt(5))*(-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) - 1 + 2*(-3/2 + sqrt(5)/2)*(1/(-sqrt(5)/2 - 1/2) - 2/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) + 4*(-1/(2*(-sqrt(5)/2 - 1/2)) + 1)/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)))/(-1 + sqrt(5)) + 6*(-3/2 + sqrt(5)/2)*(1/(-sqrt(5)/2 - 1/2) - 2/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)**2*(-sqrt(5)/2 + 5/2)))/(-1 + sqrt(5)) + 2*(-3/2 - sqrt(5)/2)*(-1/(-sqrt(5)/2 + 5/2) + 2*(-1/(2*(-sqrt(5)/2 - 1/2)) + 1)/(-sqrt(5)/2 + 5/2))/(-sqrt(5) - 1) - 6*(-3/2 - sqrt(5)/2)/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) + 12*(-3/2 - sqrt(5)/2)/((-sqrt(5) - 1)*(-sqrt(5)/2 + 5/2)) + exp(-t)
Y[,4]=c01*((1/(-sqrt(5)/2 - 1/2) - 2/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) + 4*(-1/(2*(-sqrt(5)/2 - 1/2)) + 1)/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)))*exp(t*(-3/2 - sqrt(5)/2)) + (-1/(-sqrt(5)/2 + 5/2) + 2*(-1/(2*(-sqrt(5)/2 - 1/2)) + 1)/(-sqrt(5)/2 + 5/2))*exp(t*(-3/2 + sqrt(5)/2)) - 2*exp(-t) + exp(-2*t)) + c02*(2*exp(t*(-3/2 - sqrt(5)/2))/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) + exp(t*(-3/2 + sqrt(5)/2))/(-sqrt(5)/2 + 5/2) - exp(-2*t)) + c03*((1/(-sqrt(5)/2 - 1/2) - 2/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)**2*(-sqrt(5)/2 + 5/2)))*exp(t*(-3/2 - sqrt(5)/2)) - exp(t*(-3/2 + sqrt(5)/2))/((-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2))) + c04*(2*exp(t*(-3/2 - sqrt(5)/2))/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) + exp(t*(-3/2 + sqrt(5)/2))/(-sqrt(5)/2 + 5/2)) + (-3*exp(-3*t/2)*exp(-sqrt(5)*t/2)/2 + sqrt(5)*exp(-3*t/2)*exp(-sqrt(5)*t/2)/2)*(3/(-sqrt(5)/2 - 1/2) - 6/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)**2*(-sqrt(5)/2 + 5/2))) + (-3*exp(-3*t/2)*exp(-sqrt(5)*t/2)/2 + sqrt(5)*exp(-3*t/2)*exp(-sqrt(5)*t/2)/2)*(1/(-sqrt(5)/2 - 1/2) - 2/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) + 4*(-1/(2*(-sqrt(5)/2 - 1/2)) + 1)/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2))) + 12*(-3*exp(-3*t/2)*exp(-sqrt(5)*t/2)/2 + sqrt(5)*exp(-3*t/2)*exp(-sqrt(5)*t/2)/2)/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) + (-3*exp(-3*t/2)*exp(sqrt(5)*t/2)/2 - sqrt(5)*exp(-3*t/2)*exp(sqrt(5)*t/2)/2)*(-1/(-sqrt(5)/2 + 5/2) + 2*(-1/(2*(-sqrt(5)/2 - 1/2)) + 1)/(-sqrt(5)/2 + 5/2)) - 3*(-3*exp(-3*t/2)*exp(sqrt(5)*t/2)/2 - sqrt(5)*exp(-3*t/2)*exp(sqrt(5)*t/2)/2)/((-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) + 6*(-3*exp(-3*t/2)*exp(sqrt(5)*t/2)/2 - sqrt(5)*exp(-3*t/2)*exp(sqrt(5)*t/2)/2)/(-sqrt(5)/2 + 5/2) - 5/2 - (-3/2 + sqrt(5)/2)*(3/(-sqrt(5)/2 - 1/2) - 6/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)**2*(-sqrt(5)/2 + 5/2))) - (-3/2 + sqrt(5)/2)*(1/(-sqrt(5)/2 - 1/2) - 2/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) + 4*(-1/(2*(-sqrt(5)/2 - 1/2)) + 1)/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2))) - 12*(-3/2 + sqrt(5)/2)/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) - (-3/2 - sqrt(5)/2)*(-1/(-sqrt(5)/2 + 5/2) + 2*(-1/(2*(-sqrt(5)/2 - 1/2)) + 1)/(-sqrt(5)/2 + 5/2)) + 3*(-3/2 - sqrt(5)/2)/((-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) - 6*(-3/2 - sqrt(5)/2)/(-sqrt(5)/2 + 5/2) + 2*exp(-t) + exp(-2*t)/2
R=matrix(ncol=4,nrow=length(t))
R[,1]=0
R[,2]=0
R[,3]=c01*(-2*(1/(-sqrt(5)/2 - 1/2) - 2/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) + 4*(-1/(2*(-sqrt(5)/2 - 1/2)) + 1)/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)))*exp(t*(-3/2 - sqrt(5)/2))/(-1 + sqrt(5)) - 2*(-1/(-sqrt(5)/2 + 5/2) + 2*(-1/(2*(-sqrt(5)/2 - 1/2)) + 1)/(-sqrt(5)/2 + 5/2))*exp(t*(-3/2 + sqrt(5)/2))/(-sqrt(5) - 1) - exp(-t)) + c02*(-4*exp(t*(-3/2 - sqrt(5)/2))/((-1 + sqrt(5))*(-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) - 2*exp(t*(-3/2 + sqrt(5)/2))/((-sqrt(5) - 1)*(-sqrt(5)/2 + 5/2))) + c03*(-2*(1/(-sqrt(5)/2 - 1/2) - 2/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)**2*(-sqrt(5)/2 + 5/2)))*exp(t*(-3/2 - sqrt(5)/2))/(-1 + sqrt(5)) + 2*exp(t*(-3/2 + sqrt(5)/2))/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2))) + c04*(-4*exp(t*(-3/2 - sqrt(5)/2))/((-1 + sqrt(5))*(-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) - 2*exp(t*(-3/2 + sqrt(5)/2))/((-sqrt(5) - 1)*(-sqrt(5)/2 + 5/2))) - 24*(-3*exp(-3*t/2)*exp(-sqrt(5)*t/2)/2 + sqrt(5)*exp(-3*t/2)*exp(-sqrt(5)*t/2)/2)/((-1 + sqrt(5))*(-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) - 2*(-3*exp(-3*t/2)*exp(-sqrt(5)*t/2)/2 + sqrt(5)*exp(-3*t/2)*exp(-sqrt(5)*t/2)/2)*(1/(-sqrt(5)/2 - 1/2) - 2/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) + 4*(-1/(2*(-sqrt(5)/2 - 1/2)) + 1)/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)))/(-1 + sqrt(5)) - 6*(-3*exp(-3*t/2)*exp(-sqrt(5)*t/2)/2 + sqrt(5)*exp(-3*t/2)*exp(-sqrt(5)*t/2)/2)*(1/(-sqrt(5)/2 - 1/2) - 2/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)**2*(-sqrt(5)/2 + 5/2)))/(-1 + sqrt(5)) - 2*(-3*exp(-3*t/2)*exp(sqrt(5)*t/2)/2 - sqrt(5)*exp(-3*t/2)*exp(sqrt(5)*t/2)/2)*(-1/(-sqrt(5)/2 + 5/2) + 2*(-1/(2*(-sqrt(5)/2 - 1/2)) + 1)/(-sqrt(5)/2 + 5/2))/(-sqrt(5) - 1) + 6*(-3*exp(-3*t/2)*exp(sqrt(5)*t/2)/2 - sqrt(5)*exp(-3*t/2)*exp(sqrt(5)*t/2)/2)/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) - 12*(-3*exp(-3*t/2)*exp(sqrt(5)*t/2)/2 - sqrt(5)*exp(-3*t/2)*exp(sqrt(5)*t/2)/2)/((-sqrt(5) - 1)*(-sqrt(5)/2 + 5/2)) + 24*(-3/2 + sqrt(5)/2)/((-1 + sqrt(5))*(-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) - 1 + 2*(-3/2 + sqrt(5)/2)*(1/(-sqrt(5)/2 - 1/2) - 2/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) + 4*(-1/(2*(-sqrt(5)/2 - 1/2)) + 1)/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)))/(-1 + sqrt(5)) + 6*(-3/2 + sqrt(5)/2)*(1/(-sqrt(5)/2 - 1/2) - 2/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)**2*(-sqrt(5)/2 + 5/2)))/(-1 + sqrt(5)) + 2*(-3/2 - sqrt(5)/2)*(-1/(-sqrt(5)/2 + 5/2) + 2*(-1/(2*(-sqrt(5)/2 - 1/2)) + 1)/(-sqrt(5)/2 + 5/2))/(-sqrt(5) - 1) - 6*(-3/2 - sqrt(5)/2)/((-sqrt(5) - 1)*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) + 12*(-3/2 - sqrt(5)/2)/((-sqrt(5) - 1)*(-sqrt(5)/2 + 5/2)) + exp(-t)
R[,4]=0
mod=GeneralModel(
t,
A,
c(
c01,
c02,
c03,
c04
),
inputrates,
deSolve.lsoda.wrapper
)
Yode=getC(mod)
Rode=getReleaseFlux(mod)
#begin plots
lt1=2
lt2=4
pdf(file="runit.FourpSerial_1.pdf",paper="a4")
m=matrix(c(1,2,3,4),4,1,byrow=TRUE)
layout(m)
plot(t,Y[,1],type="l",lty=lt1,col=1,ylab="Concentrations",xlab="Time")
lines(t,Yode[,1],type="l",lty=lt2,col=1)
lines(t,Y[,2],type="l",lty=lt1,col=2)
lines(t,Yode[,2],type="l",lty=lt2,col=2)
lines(t,Y[,3],type="l",lty=lt1,col=3)
lines(t,Yode[,3],type="l",lty=lt2,col=3)
lines(t,Y[,4],type="l",lty=lt1,col=4)
lines(t,Yode[,4],type="l",lty=lt2,col=4)
legend(
"topright",
c(
"anlytic sol for pool 1",
"numeric sol for pool 1",
"anlytic sol for pool 2",
"numeric sol for pool 2",
"anlytic sol for pool 3",
"numeric sol for pool 3",
"anylytic sol for pool 4",
"numeric sol for pool 4"
),
lty=c(lt1,lt2),
col=c(1,1,2,2,3,3,4,4)
)
plot(t,R[,1],type="l",lty=lt1,col=1,ylab="Respirationfluxes",xlab="Time",ylim=c(min(R),max(R)))
lines(t,Rode[,1],type="l",lty=lt2,col=1)
lines(t,R[,2],type="l",lty=lt1,col=2)
lines(t,Rode[,2],type="l",lty=lt2,col=2)
lines(t,R[,3],type="l",lty=lt1,col=3)
lines(t,Rode[,3],type="l",lty=lt2,col=3)
lines(t,R[,4],type="l",lty=lt1,col=4)
lines(t,Rode[,4],type="l",lty=lt2,col=4)
legend(
"topright",
c(
"anlytic sol for pool 1",
"numeric sol for pool 1",
"anlytic sol for pool 2",
"numeric sol for pool 2",
"anlytic sol for pool 3",
"numeric sol for pool 3",
"anylytic sol for pool 4",
"numeric sol for pool 4"
),
lty=c(lt1,lt2),
col=c(1,1,2,2,3,3,4,4)
)
dev.off()
# end plots
# begin checks
checkEquals(
Y,
Yode,
"test numeric solution for C-Content computed by the ode mehtod against analytical",
tolerance = tol,
)
checkEquals(
R,
Rode,
"test numeric solution for Respiration computed by the ode mehtod against analytical",
tolerance = tol,
)

}
```

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