OpBioGro: Optimization of dry biomass partitioning coefficients.

In serbinsh/biocro: Simulation of Energycane and Sugarcane

Description

Optimizes dry biomass partitioning coefficients using constrained optimization (see below).

Usage

  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, ...)

Arguments

phen	integer taking values 1 through 6 which indicate the phenological stage being optimized. If all of the phenological stages need to be optimized then use zero (0).
iCoef	initial vector of size 24 for the dry biomass partitioning coefficients.
WetDat	Weather data.
data	observed data.
day1	first day of the growing season.
dayn	last day of the growing season.
timestep	see BioGro
lat	see BioGro
iRhizome	see BioGro
irtl	see BioGro
canopyControl	see BioGro
seneControl	see BioGro
photoControl	see BioGro
phenoControl	see BioGro
soilControl	see BioGro
nitroControl	see BioGro
centuryControl	see BioGro
op.method	Optimization method. Whether to use optim or nlminb
verbose	Displays additional information, originally used for debugging.
...	additional arguments passed to optim or constrOptim.

Details

The optimization is done over the BioGro function. The OpBioGro function is a wrapper for optim and the constrOpBioGro is a wrapper for constrOptim.

Value

list of class OpBioGro with components

Warning

This function has not had enough testing.

References

no references yet.

See Also

BioGro constrOptim optim c4photo

Examples

## Not run: 

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)


## End(Not run)

serbinsh/biocro documentation built on May 29, 2019, 6:57 p.m.