tests/debug.r

In serbinsh/biocro: Simulation of Energycane and Sugarcane

data(weather05)

## Some coefficients
pheno.ll <- phenoParms(kLeaf1=0.48,kStem1=0.47,kRoot1=0.05,kRhizome1=-1e-4,
                       kLeaf2=0.14,kStem2=0.64,kRoot2=0.21, kRhizome2=-1e-4,
                       kLeaf3=0.01, kStem3=0.56, kRoot3=0.13, kRhizome3=0.3, 
                       kLeaf4=0.01, kStem4=0.56, kRoot4=0.13, kRhizome4=0.3,
                       kLeaf5=0.01, kStem5=0.56, kRoot5=0.13, kRhizome5=0.3,
                       kLeaf6=0.01, kStem6=0.56, kRoot6=0.13, kRhizome6=0.3)
                                 
system.time(ans <- BioGro(weather05, phenoControl = pheno.ll))

ans.dat <- as.data.frame(unclass(ans)[1:11])
sel.rows <- seq(1,nrow(ans.dat),400)
simDat <- ans.dat[sel.rows,c("ThermalT","Stem","Leaf","Root","Rhizome","Grain","LAI")]
plot(ans,simDat)

## Residual sum of squares before the optimization

ans0 <- BioGro(weather05)
RssBioGro(simDat,ans0)


op1.mc <- MCMCBioGro(phen=1, niter=2,niter2=2,
##                     day1=130,dayn=140,
                     WetDat=weather05,
                     data=simDat)


plot(op1.mc)

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