mOpc4photo: Multiple optimization of C4 photosynthesis.
In BioCro: Simulation of Biomass Crops

Description Usage Arguments Details Value Author(s) See Also Examples

Wrapper function that allows for optimization of multiple A/Ci or A/Q curves.

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mOpc4photo(data, ID = NULL, ivmax = 39, ialpha = 0.04,
iRd = 0.8, ikparm = 0.7, itheta = 0.83, ibeta = 0.93, curve.kind =
c("Q", "Ci"), op.level = 1, op.ci = FALSE, verbose = FALSE, ...)

`data`	observed assimilation data, which should be a data frame or matrix. The first column should contain a run or id. The second column should be observed net assimilation rate (μ mol m^{-2} s^{-1}). The third column should be the observed quantum flux (μ mol m^{-2} s^{-1}). The fourth column should be observed temperature of the leaf (Celsius). The fifth column should be the observed relative humidity in proportion (e.g. 0.7). An optional sixth column can contain atmospheric CO2.
`ID`	Optional vector with an alternative ID tothe one used in data for runs. The length shoudl be equal to the number of runs.
`ivmax`	Initial value for vmax. It can be a single value or a vector of length equal to the number of runs.
`ialpha`	Initial value for alpha. It can be a single value or a vector of length equal to the number of runs.
`iRd`	Initial value for vmax. It can be a single value or a vector of length equal to the number of runs.
`ikparm`	Initial value for vmax. It can be a single value or a vector of length equal to the number of runs.
`itheta`	Initial value for vmax. It can be a single value or a vector of length equal to the number of runs.
`ibeta`	Initial value for vmax. It can be a single value or a vector of length equal to the number of runs.
`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.
`op.ci`	Whether to optimize intercellular CO2. Default is FALSE as 'fast-measured' light curves do not provide reliable values of Ci.
`verbose`	Whether to display output about convergence of each run.
`...`	Used to supply additional arguments to `Opc4photo`.

There are printing and plotting methods for the object created by this function. The plotting function has an argument that it is used to dsiplay either vmax or alpha (i.e. parm=c("vmax","alpha")). In both cases the optimized value plus confidence intervals will be displayed for each run.

An object of class mOpc4photo

`mat`	Matrix with optimized parameters.
`op.level`	Optimization level..
`ciVmax`	confidence intervals for vmax.
`ciAlpha`	confidence intervals for alpha.
`curve.kind`	Whether A/Ci or A/Q curves were optimized.