biocro: Simulation of Energycane and Sugarcane

## /R/c3photo.R by Fernando Ezequiel Miguez Copyright (C) 2009-2010
## 
## This program is free software; you can redistribute it and/or modify it
## under the terms of the GNU General Public License as published by the Free
## Software Foundation; either version 2 or 3 of the License (at your option).
## 
## This program is distributed in the hope that it will be useful, but WITHOUT
## ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
## FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for
## more details.
## 
## A copy of the GNU General Public License is available at
## http://www.r-project.org/Licenses/
##' Simulates C3 photosynthesis
##'
##' Simulates coupled assimilation and stomatal conductance based on Farquhar
##' and Ball-Berry.
##'
##' ~~ If necessary, more details than the description above ~~
##'
##' @param Qp Quantum flux
##' @param Tl Leaf temperature
##' @param RH Relative humidity (fraction -- 0-1)
##' @param vcmax Maximum rate of carboxylation
##' @param jmax Maximum rate of electron transport
##' @param Rd Leaf dark respiration
##' @param Catm Atmospheric carbon dioxide.
##' @param O2 Atmospheric Oxygen concentration (mmol/mol)
##' @param b0 Intercept for the Ball-Berry model
##' @param b1 Slope for the Ball-Berry model
##' @param theta Curvature parameter
##' @export
##' @return A list
##' @returnItem Gs Stomatal Conductance
##' @returnItem Assim CO2 Assimilation
##' @returnItem Ci Intercellular CO2
##' @note ~~further notes~~ ## Additional notes about assumptions
##' @author Fernando E. Miguez
##' @seealso See Also \code{\link{Opc3photo}}
##' @references
##'
##' Farquhar (1980) Ball-Berry (1987)
##' @keywords models
##' @examples
##'
##'
##' ## Testing the c3photo function
##' ## First example: looking at the effect of changing Vcmax
##' Qps <- seq(0,2000,10)
##' Tls <- seq(0,55,5)
##' rhs <- c(0.7)
##' dat1 <- data.frame(expand.grid(Qp=Qps,Tl=Tls,RH=rhs))
##'
##' res1 <- c3photo(dat1$Qp,dat1$Tl,dat1$RH) ## default Vcmax = 100
##' res2 <- c3photo(dat1$Qp,dat1$Tl,dat1$RH,vcmax=120)
##'
##' ## Plot comparing alpha 0.04 vs. 0.06 for a range of conditions
##' xyplot(res1$Assim + res2$Assim ~ Qp | factor(Tl) , data = dat1,
##'             type='l',col=c('blue','green'),lwd=2,
##'             ylab=expression(paste('Assimilation (',
##'                  mu,mol,' ',m^-2,' ',s^-1,')')),
##'              xlab=expression(paste('Quantum flux (',
##'                  mu,mol,' ',m^-2,' ',s^-1,')')),
##'             key=list(text=list(c('Vcmax 100','Vcmax 120')),
##'               lines=TRUE,col=c('blue','green'),lwd=2))
##'
##' ## Second example: looking at the effect of changing Jmax
##' ## Plot comparing Jmax 300 vs. 100 for a range of conditions
##'
##' res1 <- c3photo(dat1$Qp,dat1$Tl,dat1$RH) ## default Jmax = 300
##' res2 <- c3photo(dat1$Qp,dat1$Tl,dat1$RH,jmax=100)
##'
##' xyplot(res1$Assim + res2$Assim ~ Qp | factor(Tl) , data = dat1,
##'            type='l',col=c('blue','green'),lwd=2,
##'             ylab=expression(paste('Assimilation (',
##'                  mu,mol,' ',m^-2,' ',s^-1,')')),
##'              xlab=expression(paste('Quantum flux (',
##'                  mu,mol,' ',m^-2,' ',s^-1,')')),
##'             key=list(text=list(c('Jmax 300','Jmax 100')),
##'               lines=TRUE,col=c('blue','green'),lwd=2))
##'
##' ## A/Ci curve
##'
##' Ca <- seq(20,1000,length.out=50)
##' dat2 <- data.frame(Qp=rep(700,50), Tl=rep(25,50), rh=rep(0.7,50))
##' res1 <- c3photo(dat2$Qp, dat2$Tl, dat2$rh, Catm = Ca)
##' res2 <- c3photo(dat2$Qp, dat2$Tl, dat2$rh, Catm = Ca, vcmax = 70)
##'
##' xyplot(res1$Assim ~ res1$Ci,
##'            lwd=2,
##'            panel = function(x,y,...){
##'                    panel.xyplot(x,y,type='l',col='blue',...)
##'                    panel.xyplot(res2$Ci,res2$Assim, type='l', col =
##'            'green',...)
##'            },
##'             ylab=expression(paste('Assimilation (',
##'                  mu,mol,' ',m^-2,' ',s^-1,')')))
##'
##'
##'
c3photo <- function(Qp, Tl, RH, vcmax = 100, jmax = 180, Rd = 1.1, Catm = 380, O2 = 210, 
    b0 = 0.08, b1 = 5, theta = 0.7) {
    if ((length(Qp) != length(Tl)) || (length(Qp) != length(RH))) 
        stop("the lengths of the Qp, Tl and RH vectors should be equal")
    
    
    if (max(RH) > 1) 
        stop("RH should be between 0 and 1")
    ## if(Catm < 20) warning('Stomatal conductance is not reliable for values of
    ## Catm lower than 20\n') if(Catm < 15) stop('Assimilation is not reliable for
    ## low (<15) Catm values')
    
    
    if (length(Catm) == 1) {
        Catm <- rep(Catm, length(Qp))
    } else {
        if (length(Catm) != length(Qp)) 
            stop("length of Catm should be either 1 or equal to length of Qp")
    }
    res <- .Call(c3photo_sym, as.double(Qp), as.double(Tl), as.double(RH), as.double(vcmax), 
        as.double(jmax), as.double(Rd), as.double(Catm), as.double(b0), as.double(b1), 
        as.double(O2), as.double(theta))
    res
}