mOpc3photo: Multiple optimization of assimilation (or stomatal...

In BioCro: Simulation of Biomass Crops

Description

It is a wrapper for Opc3photo which allows for optimization of multiple runs of curves (A/Q or A/Ci).

Usage

mOpc3photo(data, ID=NULL, iVcmax = 100, iJmax = 180, iRd = 1.1,
           op.level = 1, curve.kind = c("Ci","Q"), verbose = FALSE, ...)

Arguments

data	should be a data.frame or matrix with x columns col 1: should be an ID for the different runs col 2: measured assimilation (CO2 uptake) col 3: Incomming PAR (photosynthetic active radiation) col 4: Leaf temperature col 5: Relative humidity col 6: Intercellular CO2 (for A/Ci curves) col 7: Reference CO2 level
ID	optional argument to include ids. should be of length equal to the number of runs.
iVcmax	Single value or vector of length equal to number of runs to supply starting values for the optimization of vcmax.
iJmax	Single value or vector of length equal to number of runs to supply starting values for the optimization of jmax.
iRd	Single value or vector of length equal to number of runs to supply starting values for the optimization of Rd.
op.level	Level 1 will optimize Vcmax and Jmax and level 2 will optimize Vcmax, Jmax and Rd.
curve.kind	Whether an A/Ci curve is being optimized or an A/Q curve.
verbose	Whether to print information about progress.
...	Additional arguments to be passed to Opc3photo

Details

Include more details about the data.

Value

an object of class 'mOpc3photo'

if op.level equals 1 best Vcmax, Jmax and convergence

if op.level equals 2 best Vcmax, Jmax, Rd and convergence

Author(s)

Fernando E. Miguez

See Also

See also Opc3photo

Examples

data(simAssim)
simAssim <- cbind(simAssim[,1:6],Catm=simAssim[,10])
simAssim <- simAssim[simAssim[,1] < 11,]

plotAC(simAssim, trt.col=1)

op.all <- mOpc3photo(simAssim, op.level=1,
                      verbose=TRUE)

plot(op.all)
plot(op.all, parm="jmax")

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