Opc3photo: Optimize parameters of the C3 photosynthesis model.

In BioCro: Simulation of Biomass Crops

Description

Applies the optim function to C3 photosynthesis.

Usage

Opc3photo(data, ivcmax = 100, ijmax = 180, iRd = 1.1, Catm = 380, 
    O2 = 210, ib0 = 0.08, ib1 = 9.58, itheta = 0.7, op.level = 1, 
    op.method = c("optim", "nlminb"), response = c("Assim", "StomCond"), 
    level = 0.95, hessian = TRUE, curve.kind = c("Ci", "Q"), 
    op.ci = FALSE, ...)

Arguments

For Opc3photo:

data	should be a data.frame or matrix with x columns col 1: measured assimilation (CO2 uptake) col 2: Incomming PAR (photosynthetic active radiation) col 3: Leaf temperature col 4: Relative humidity col 5: Intercellular CO2 (for A/Ci curves) col 6: Reference CO2 level
ivcmax	Initial value for vcmax.
ijmax	Initial value for jmax.
iRd	Initial value for Rd.
Catm	Reference CO2.
O2	Reference level of O2.
ib0	Initial value for the intercept to the Ball-Berry model.
ib1	Initial value for the slope to the Ball-Berry model.
itheta	Initial value for theta.
op.level	Level 1 will optimize Vcmax and Jmax and level 2 will optimize Vcmax, Jmax and Rd.
op.method	optimization method. At the moment only optim is implemented.
response	"Assim" for assimilation and "StomCond" for stomatal conductance.
level	Confidence interval level.
hessian	Whether the hessian should be computed
curve.kind	Whether an A/Ci curve is being optimized or an A/Q curve.
op.ci	whether to optimize intercellular CO2.
...	Additioanl arguments to be passed to optim.

Value

An object of class Opc3photo.

The following components can be extracted:

bestVmax	optimized vmax.
bestJmax	optimized jmax.
ReSumS	Residual Sum of Squares.
Convergence	Convergence status.
VarCov	Variance-covariance matrix.
df	degress of freedom.
ciVmax	Confidence interval for vmax.
ciJmax	Confidence interval for jmax.
corVJ	correlation between vmax and jmax.
level	Confidence interval level.
data	Original data.
xparms	Additional parameters.
curve.kind	A/Ci or A/Q curve.
op.level	Level 1 means vcmax and jmax were optimized and level 2 vcmax, jmax and Rd.
response	"Assim" or "StomCond".

Note

~~further notes~~ Additional notes about the assumptions.

Author(s)

Fernando E. Miguez

See Also

See Also mOpc3photo

Examples

## Load fabricated data
data(simA100)
## Look at it
head(simA100)

op <- Opc3photo(simA100[,1:5],Catm=simA100[,9], op.level = 2)

## If faced with a difficult problem
## This can give starting values
op100 <- Opc3photo(simA100[,1:5],Catm=simA100[,9],
                   op.level = 2, method="SANN",
                   hessian=FALSE)

op100 <- Opc3photo(simA100[,1:5],Catm = simA100[,9],
                   op.level = 2, 
                   ivcmax = op100$bestVmax,
                   ijmax = op100$bestJmax,
                   iRd = op100$bestRd)
op100

BioCro documentation built on May 2, 2019, 6:15 p.m.