Description Usage Arguments Value See Also Examples
Optimization method for the Collatz C4 photosynthesis model. At the moment Vcmax and alpha are optimized only.
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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 |
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. |
iStomWS |
initial value for the stomata water stress factor. |
ws |
|
response |
Use |
curve.kind |
If |
op.level |
optimization level. If equal to 1
|
level |
level for the confidence intervals. |
hessian |
Whether the hessian matrix should be
computed. See |
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
|
An object of class Opc4photo
a list
with components
If op.level
2 bestRd
will also be supplied.
If op.level
3 theta
and bestRd
will
also be supplied.
If op.level
2 ciRd
will also be supplied.
If op.level
3 ciTheta
and ciRd
will
also be supplied.
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