OpBioGro(phen = 1, iCoef = NULL, WetDat, data, day1 = NULL, dayn = NULL, timestep = 1, lat = 40, iRhizome = 7, irtl = 1e-04, canopyControl = list(), seneControl = list(), photoControl = list(), phenoControl = list(), soilControl = list(), nitroControl = list(), centuryControl = list(), op.method = c("optim", "nlminb"), verbose = FALSE, ...)
BioGroBioGroBioGroBioGroBioGroBioGroBioGroBioGroBioGroBioGroBioGrooptim or constrOptim.list of class OpBioGro with components
Optimizes dry biomass partitioning coefficients using constrained optimization (see below).
The optimization is done over the BioGro
function. The OpBioGro function is a wrapper for
optim and the constrOpBioGro is a wrapper for
constrOptim.
This function has not had enough testing.
no references yet.
## <strong>Not run</strong>: # # data(weather05) # # ## Some coefficients # pheno.ll <- phenoParms(kLeaf1=0.48,kStem1=0.47,kRoot1=0.05,kRhizome1=-1e-4, # kLeaf2=0.14,kStem2=0.65,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),length.out=8) # 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) # # ## This will optimize only the first phenological stage # idb <- valid_dbp(idbp(simDat)) # op1 <- OpBioGro(phen=0, WetDat=weather05, data = simDat, iCoef=idb) # ## or # cop1 <- constrOpBioGro(phen=0, WetDat=weather05, data = simDat) # # ## <strong>End(Not run)</strong>