Optimization of C4 photosynthesis parameters

Usage

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, iStomWS = 1, ws = c("gs", "vmax"), iupperT = 37.5, ilowerT = 3, response = c("Assim", "StomCond"), curve.kind = c("Q", "Ci"), op.level = 1, level = 0.95, hessian = TRUE, op.ci = FALSE, ...)

Arguments

data

observed assimilation data, which should be a data frame or matrix. The first column should be observed net assimilation rate (\mu mol m^{-2} s^{-1}). The second column should be the observed quantum flux (\mu 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 \mumol/mol).

ib0

initial value for the Ball-Berry intercept.

ib1

initial value for the Ball-Berry slope.

iStomWS

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.

list()

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.

Examples

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


Optimization of C4 photosynthesis

		 95 %   Conf Int
          best    lower    upper
Vmax    31.326   30.815   31.838
alpha    0.054    0.052    0.056

 Corr  Vmax and alpha: -0.4754783 

 Resid Sums Sq: 0.9731662 

Convergence:YES


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

See also