Opc4photo: Optimization of C4 photosynthesis parameters
In BioCro: Simulation of Biomass Crops

Description Usage Arguments Value See Also Examples

Optimization method for the Collatz C4 photosynthesis model. At the moment Vcmax and alpha are optimized only.

Opc4photo(data, ivmax = 39, ialpha = 0.04, iRd = 0.8, ikparm = 0.7, 
    itheta = 0.83, ibeta = 0.93, Catm = 380, ib0 = 0.08, ib1 = 3, 
    istress = 1, ws = c("gs", "vmax"), response = c("Assim", 
        "StomCond"), curve.kind = c("Q", "Ci"), op.level = 1, 
    level = 0.95, hessian = TRUE, op.ci = FALSE, ...)

`data`	observed assimilation data, which should be a data frame or matrix. The first column should be observed net assimilation rate (μ mol m^{-2} s^{-1}). The second column should be the observed quantum flux (μ mol m^{-2} s^{-1}). The third column should be observed temperature of the leaf (Celsius). The fourth column should be the observed relative humidity in proportion (e.g. 0.7). An optional fifth column can contain intercellular CO2. The reference level of CO2 should be supplied to the function using the `Catm` argument.
`ivmax`	initial value for Vcmax (default = 39).
`ialpha`	initial value for alpha (default = 0.04).
`iRd`	initial value for dark respiration (default = 0.8).
`ikparm`	initial value for k (default = 0.7).
`itheta`	initial value for theta (default = 0.83).
`ibeta`	initial value for beta (default = 0.93).
`Catm`	Atmospheric CO2 in ppm (or μmol/mol).
`ib0`	initial value for the Ball-Berry intercept.
`ib1`	initial value for the Ball-Berry slope.
`istress`	initial value for the stomata water stress factor.
`ws`	`ws` flag. See `c4photo`.
`response`	Use `"Assim"` if you want to optimize assimilation data and use `"StomCond"` if you want to optimize stomatal conductance data. The parameters optimized will be different.
`curve.kind`	If `"Q"` a type of response which mainly depends on light will be assumed. Typically used to optimized light response curves or diurnals. Use `"Ci"` for A/Ci curves (stomatal conductance could also be optimized).
`op.level`	optimization level. If equal to 1 `vmax` and `alpha` will be optimized. If 2, `vmax`, `alpha` and `Rd` will be optimized. If 3, `vmax`, `alpha`, `theta` and `Rd` will be optimized.
`level`	level for the confidence intervals.
`hessian`	Whether the hessian matrix should be computed. See `optim`.
`op.ci`	Whether to optimize intercellular CO2. Default is FALSE as 'fast-measured' light curves do not provide reliable values of Ci.
`...`	Additional arguments passed to the `optim` in particular if a lower or upper bound is desired this could be achieved by adding `lower=c(0,0)` this will impose a lower bound on `vmax` and `alpha` of zero so preventing negative values from being returned. When the lower argument is added the optimization method changes from Nelder-Mead to BFGS.

An object of class Opc4photo a list with components

`bestVcmax`	optimized value for `Vmax`
`bestAlpha`	optimized value for `alpha`

If op.level 2 bestRd will also be supplied. If op.level 3 theta and bestRd will also be supplied.

`ReSumS`	Residual Sum of Squares
`Convergence`	Integer indicating convergence 0 is succesful convergence. See the `optim` function for details.
`VarCov`	Variance-Covariance matrix
`df`	degrees of freedom
`ciVmax`	Confidence interval for Vmax
`ciAlpha`	Confidence interval for Alpha

If op.level 2 ciRd will also be supplied. If op.level 3 ciTheta and ciRd will also be supplied.

`corVA`	correlation between Vmax and Alpha
`level`	level for the confidence interval
`data`	data.frame with the original data
`op.level`	optimization level
`response`	type of response either assimilation or stomatal conductance
`curve.kind`	whether it is `"Q"` or `"Ci"`

c4photo optim

data(aq)
## Select data for a single AQ optimization
aqd <- data.frame(aq[aq[,1] == 6,-c(1:2)],Catm=400)
res <- Opc4photo(aqd, Catm=aqd$Catm)
res

plot(res, plot.kind = "OandF", type='o')