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*(-1/(-sqrt(5)/2 - 1/2) + 1)/((1 + sqrt(5))*(-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 - 1/2) + 1)*exp(t*(-3/2 + sqrt(5)/2))/((1 + sqrt(5))*(-sqrt(5)/2 + 5/2)) - exp(-t)) + c02*(4*exp(t*(-3/2 - sqrt(5)/2))/((-1 + sqrt(5))*(1 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) + 2*exp(t*(-3/2 + sqrt(5)/2))/((1 + sqrt(5))*(-sqrt(5)/2 + 5/2))) + c03*(-2*(1/(-sqrt(5)/2 - 1/2) + 2/((1 + sqrt(5))*(-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))/((1 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2))) + c04*(4*exp(t*(-3/2 - sqrt(5)/2))/((-1 + sqrt(5))*(1 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) + 2*exp(t*(-3/2 + sqrt(5)/2))/((1 + sqrt(5))*(-sqrt(5)/2 + 5/2))) + 12*(1/(-sqrt(5)/2 - 1/2) + 2/((1 + sqrt(5))*(-sqrt(5)/2 - 1/2)**2*(-sqrt(5)/2 + 5/2)))*exp(t*(-3/2 - sqrt(5)/2))/((-1 + sqrt(5))*(sqrt(5) + 3)) + 4*(1/(-sqrt(5)/2 - 1/2) - 2*(-1/(-sqrt(5)/2 - 1/2) + 1)/((1 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)))*exp(t*(-3/2 - sqrt(5)/2))/((-1 + sqrt(5))*(sqrt(5) + 3)) - 48*exp(t*(-3/2 - sqrt(5)/2))/((-1 + sqrt(5))*(1 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)*(sqrt(5) + 3)) + 24*exp(t*(-3/2 + sqrt(5)/2))/((-3 + sqrt(5))*(1 + sqrt(5))*(-sqrt(5)/2 + 5/2)) - 12*exp(t*(-3/2 + sqrt(5)/2))/((-3 + sqrt(5))*(1 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) + 4*(-1/(-sqrt(5)/2 - 1/2) + 1)*exp(t*(-3/2 + sqrt(5)/2))/((-3 + sqrt(5))*(1 + sqrt(5))*(-sqrt(5)/2 + 5/2)) + 48/((-1 + sqrt(5))*(1 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)*(sqrt(5) + 3)) - 1 - 4*(1/(-sqrt(5)/2 - 1/2) - 2*(-1/(-sqrt(5)/2 - 1/2) + 1)/((1 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)))/((-1 + sqrt(5))*(sqrt(5) + 3)) - 12*(1/(-sqrt(5)/2 - 1/2) + 2/((1 + sqrt(5))*(-sqrt(5)/2 - 1/2)**2*(-sqrt(5)/2 + 5/2)))/((-1 + sqrt(5))*(sqrt(5) + 3)) - 4*(-1/(-sqrt(5)/2 - 1/2) + 1)/((-3 + sqrt(5))*(1 + sqrt(5))*(-sqrt(5)/2 + 5/2)) + 12/((-3 + sqrt(5))*(1 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) - 24/((-3 + sqrt(5))*(1 + sqrt(5))*(-sqrt(5)/2 + 5/2)) + exp(-t)
   Y[,4]=c01*((1/(-sqrt(5)/2 - 1/2) - 2*(-1/(-sqrt(5)/2 - 1/2) + 1)/((1 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)))*exp(t*(-3/2 - sqrt(5)/2)) + (-1/(-sqrt(5)/2 - 1/2) + 1)*exp(t*(-3/2 + sqrt(5)/2))/(-sqrt(5)/2 + 5/2) - 2*exp(-t) + exp(-2*t)) + c02*(-2*exp(t*(-3/2 - sqrt(5)/2))/((1 + sqrt(5))*(-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/((1 + sqrt(5))*(-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))/((1 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) + exp(t*(-3/2 + sqrt(5)/2))/(-sqrt(5)/2 + 5/2)) + 24*exp(t*(-3/2 - sqrt(5)/2))/((1 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)*(sqrt(5) + 3)) - 2*(1/(-sqrt(5)/2 - 1/2) - 2*(-1/(-sqrt(5)/2 - 1/2) + 1)/((1 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)))*exp(t*(-3/2 - sqrt(5)/2))/(sqrt(5) + 3) - 2*(3/(-sqrt(5)/2 - 1/2) + 6/((1 + sqrt(5))*(-sqrt(5)/2 - 1/2)**2*(-sqrt(5)/2 + 5/2)))*exp(t*(-3/2 - sqrt(5)/2))/(sqrt(5) + 3) + 12*exp(t*(-3/2 + sqrt(5)/2))/((-3 + sqrt(5))*(-sqrt(5)/2 + 5/2)) - 6*exp(t*(-3/2 + sqrt(5)/2))/((-3 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) + 2*(-1/(-sqrt(5)/2 - 1/2) + 1)*exp(t*(-3/2 + sqrt(5)/2))/((-3 + sqrt(5))*(-sqrt(5)/2 + 5/2)) - 5/2 + 2*(3/(-sqrt(5)/2 - 1/2) + 6/((1 + sqrt(5))*(-sqrt(5)/2 - 1/2)**2*(-sqrt(5)/2 + 5/2)))/(sqrt(5) + 3) + 2*(1/(-sqrt(5)/2 - 1/2) - 2*(-1/(-sqrt(5)/2 - 1/2) + 1)/((1 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)))/(sqrt(5) + 3) - 24/((1 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)*(sqrt(5) + 3)) - 2*(-1/(-sqrt(5)/2 - 1/2) + 1)/((-3 + sqrt(5))*(-sqrt(5)/2 + 5/2)) + 6/((-3 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) - 12/((-3 + sqrt(5))*(-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*(-1/(-sqrt(5)/2 - 1/2) + 1)/((1 + sqrt(5))*(-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 - 1/2) + 1)*exp(t*(-3/2 + sqrt(5)/2))/((1 + sqrt(5))*(-sqrt(5)/2 + 5/2)) - exp(-t)) + c02*(4*exp(t*(-3/2 - sqrt(5)/2))/((-1 + sqrt(5))*(1 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) + 2*exp(t*(-3/2 + sqrt(5)/2))/((1 + sqrt(5))*(-sqrt(5)/2 + 5/2))) + c03*(-2*(1/(-sqrt(5)/2 - 1/2) + 2/((1 + sqrt(5))*(-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))/((1 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2))) + c04*(4*exp(t*(-3/2 - sqrt(5)/2))/((-1 + sqrt(5))*(1 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) + 2*exp(t*(-3/2 + sqrt(5)/2))/((1 + sqrt(5))*(-sqrt(5)/2 + 5/2))) + 12*(1/(-sqrt(5)/2 - 1/2) + 2/((1 + sqrt(5))*(-sqrt(5)/2 - 1/2)**2*(-sqrt(5)/2 + 5/2)))*exp(t*(-3/2 - sqrt(5)/2))/((-1 + sqrt(5))*(sqrt(5) + 3)) + 4*(1/(-sqrt(5)/2 - 1/2) - 2*(-1/(-sqrt(5)/2 - 1/2) + 1)/((1 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)))*exp(t*(-3/2 - sqrt(5)/2))/((-1 + sqrt(5))*(sqrt(5) + 3)) - 48*exp(t*(-3/2 - sqrt(5)/2))/((-1 + sqrt(5))*(1 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)*(sqrt(5) + 3)) + 24*exp(t*(-3/2 + sqrt(5)/2))/((-3 + sqrt(5))*(1 + sqrt(5))*(-sqrt(5)/2 + 5/2)) - 12*exp(t*(-3/2 + sqrt(5)/2))/((-3 + sqrt(5))*(1 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) + 4*(-1/(-sqrt(5)/2 - 1/2) + 1)*exp(t*(-3/2 + sqrt(5)/2))/((-3 + sqrt(5))*(1 + sqrt(5))*(-sqrt(5)/2 + 5/2)) + 48/((-1 + sqrt(5))*(1 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)*(sqrt(5) + 3)) - 1 - 4*(1/(-sqrt(5)/2 - 1/2) - 2*(-1/(-sqrt(5)/2 - 1/2) + 1)/((1 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)))/((-1 + sqrt(5))*(sqrt(5) + 3)) - 12*(1/(-sqrt(5)/2 - 1/2) + 2/((1 + sqrt(5))*(-sqrt(5)/2 - 1/2)**2*(-sqrt(5)/2 + 5/2)))/((-1 + sqrt(5))*(sqrt(5) + 3)) - 4*(-1/(-sqrt(5)/2 - 1/2) + 1)/((-3 + sqrt(5))*(1 + sqrt(5))*(-sqrt(5)/2 + 5/2)) + 12/((-3 + sqrt(5))*(1 + sqrt(5))*(-sqrt(5)/2 - 1/2)*(-sqrt(5)/2 + 5/2)) - 24/((-3 + sqrt(5))*(1 + sqrt(5))*(-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,
   )

 }