Optimize parameters of the C3 photosynthesis model.

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

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.

Examples

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

          Assim   Qp Tl  RH        Ci    Vcmax     Jmax       Rd Catm
[1,] -0.6944929 1500 25 0.7  4.653977 90.80678 205.9745 2.311849    0
[2,] -0.6944929 1500 25 0.7  9.653877 90.80678 205.9745 2.311849    5
[3,] -0.6944929 1500 25 0.7 14.653877 90.80678 205.9745 2.311849   10
[4,] -0.6944929 1500 25 0.7 24.653877 90.80678 205.9745 2.311849   20
[5,] -0.6944929 1500 25 0.7 34.653877 90.80678 205.9745 2.311849   30
[6,]  0.4378667 1500 25 0.7 52.389158 90.80678 205.9745 2.311849   50


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


Optimization of C3 photosynthesis

		 95 %   Conf Int
         best    lower   upper
Vmax    90.63    90.09    91.2
Jmax   170.67   169.95   171.4
Rd       0.65     0.59     0.7

 Corr  Vmax and Jmax: 0.2618421 

 Resid Sums Sq: 0.09047036 

Convergence:YES

See also

Author