RsqC4photo: R-squared for C4 photosynthesis simulation (Collatz model)
In serbinsh/biocro: Simulation of Energycane and Sugarcane

Description Usage Arguments Value Examples

This is an auxiliary function which is made available in case it is useful. It calculates the R-squared based on observed assimilation (or stomatal conductance) data and coefficients for the Collatz C4 photosynthesis model. The only coefficients being considered are Vcmax and alpha as described in the Collatz paper. At the moment it does not optimize k; this will be added soon. Notice that to be able to optimize k A/Ci type data are needed.

  RsqC4photo(data, vmax = 39, alph = 0.04, kparm = 0.7,
    theta = 0.83, beta = 0.93, Rd = 0.8, Catm = 380,
    b0 = 0.08, b1 = 3, StomWS = 1,
    response = c("Assim", "StomCond"))

`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).
`vmax`	Vcmax (default = 39); for more details see the `c4photo` function.
`alph`	alpha as in Collatz (default = 0.04); for more details see the `c4photo` function.
`kparm`	k as in Collatz (default = 0.70); for more details see the `c4photo` function.
`theta`	theta as in Collatz (default = 0.83); for more details see the `c4photo` function.
`beta`	beta as in Collatz (default = 0.93); for more details see the `c4photo` function.
`Rd`	Rd as in Collatz (default = 0.8); for more details see the `c4photo` function.
`StomWS`	StomWS as in Collatz (default = 1); for more details see the `c4photo` function.
`Catm`	Atmospheric CO2 in ppm (or μmol/mol).
`b0`	Intercept for the Ball-Berry model.
`b1`	Slope for the Ball-Berry model.
`response`	Use `'Assim'` if you want an R^2 for assimilation data and use `'StomCond'` if you want an R^2 for stomatal conductance data.

a numeric object

It simply returns the R^2 value for the given data and coefficients.

data(obsNaid)
## These data are from Naidu et al. (2003)
## in the correct format
res <- RsqC4photo(obsNaid)
## Other example using Beale, Bint and Long (1996)
data(obsBea)
resB <- RsqC4photo(obsBea)