c4photo: Coupled photosynthesis-stomatal conductance simulation
In serbinsh/biocro: Simulation of Energycane and Sugarcane

Description Usage Arguments Value References See Also Examples

The mathematical model is based on Collatz et al (1992) (see References). Stomatal conductance is based on code provided by Joe Berry.

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  c4photo(Qp, Tl, RH, vmax = 39, alpha = 0.04, kparm = 0.7,
    theta = 0.83, beta = 0.93, Rd = 0.8, Catm = 380,
    b0 = 0.08, b1 = 3, StomWS = 1, ws = c("gs", "vmax"))

`Qp`	quantum flux (direct light), (micro mol m-2 s-1).
`Tl`	temperature of the leaf (Celsius).
`RH`	relative humidity (as a fraction, i.e. 0-1).
`vmax`	maximum carboxylation of Rubisco according to the Collatz model.
`alpha`	alpha parameter according to the Collatz model. Initial slope of the response to Irradiance.
`kparm`	k parameter according to the Collatz model. Initial slope of the response to CO2.
`theta`	theta parameter according to the Collatz model. Curvature for light response.
`beta`	beta parameter according to the Collatz model. Curvature for response to CO2.
`Rd`	Rd parameter according to the Collatz model. Dark respiration.
`Catm`	Atmospheric CO2 in ppm (or micromol/mol).
`b0`	intercept for the Ball-Berry stomatal conductance model.
`b1`	slope for the Ball-Berry stomatal conductance model.
`StomWS`	coefficient which controls the effect of water stress on stomatal conductance and assimilation.
`ws`	option to control whether the water stress factor is applied to stomatal conductance ('gs') or to Vmax ('vmax').

a list structure with components

G. Collatz, M. Ribas-Carbo, J. Berry. (1992). Coupled photosynthesis-stomatal conductance model for leaves of C4 plants. Australian Journal of Plant Physiology 519–538.

eC4photo

## Not run: 
     ## First example: looking at the effect of changing alpha
      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 <- c4photo(dat1$Qp,dat1$Tl,dat1$RH) ## default alpha = 0.04
      res2 <- c4photo(dat1$Qp,dat1$Tl,dat1$RH,alpha=0.06)

     ## 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('alpha 0.04','alpha 0.06')),
              lines=TRUE,col=c('blue','green'),lwd=2))

     ## Second example: looking at the effect of changing vmax
     ## Plot comparing Vmax 39 vs. 50 for a range of conditions

      res1 <- c4photo(dat1$Qp,dat1$Tl,dat1$RH) ## default Vmax = 39
      res2 <- c4photo(dat1$Qp,dat1$Tl,dat1$RH,vmax=50)

     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('Vmax 39','Vmax 50')),
              lines=TRUE,col=c('blue','green'),lwd=2))

     ## Small effect of low RH on  Assim
      Qps <- seq(0,2000,10)
      Tls <- seq(0,55,5)
      rhs <- c(0.2,0.9)
      dat1 <- data.frame(expand.grid(Qp=Qps,Tl=Tls,RH=rhs))
      res1 <- c4photo(dat1$Qp,dat1$Tl,dat1$RH)
     # plot for Assimilation and two RH
      xyplot(res1$Assim ~ Qp | factor(Tl) , data = dat1,
             groups=RH, 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('RH 20%','RH 90%')),
                        lines=TRUE,col=c('blue','green'),
                        lwd=2))

    ## Effect of the previous runs on Stomatal conductance

    x11() # opens a new plotting device
    xyplot(res1$Gs ~ Qp | factor(Tl) , data = dat1,
           type='l', groups=RH,
           col=c('blue','green'),lwd=2,
           ylab=expression(paste('Stomatal Conductance (',
                           mu,mol,' ',m^-2,' ',s^-1,')')),
           xlab=expression(paste('Quantum flux (',
                           mu,mol,' ',m^-2,' ',s^-1,')')),
           key=list(text=list(c('RH 20%','RH 90%')),
                     lines=TRUE,col=c('blue','green'),
                     lwd=2))


## A Ci curve for the Collatz model
## Assuming constant values of Qp, Temp, and RH
## Notice the effect of the different kparm
## The loop is needed because the length of Ca
## should be the same as Qp

Ca <- seq(15,400,5)

res1 <- numeric(length(Ca))
res2 <- numeric(length(Ca))
for(i in 1:length(Ca)){
  res1[i] <- c4photo(1500,25,0.7,Catm=Ca[i])$Assim
  res2[i] <- c4photo(1500,25,0.7,Catm=Ca[i],kparm=0.8)$Assim
}

xyplot(res1 + res2 ~ Ca ,type='l',lwd=2,
       col=c('blue','green'),
     xlab=expression(paste(CO[2],' (ppm)')),
     ylab=expression(paste('Assimilation (',
         mu,mol,' ',m^-2,' ',s^-1,')')),
     key=list(text=list(c('kparm 0.7','kparm 0.8')),
                        lines=TRUE,col=c('blue','green'),
                        lwd=2))

## Effect of Reduction in Assimilation due to
## water stress

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 <- c4photo(dat1$Qp,dat1$Tl,dat1$RH) ## default StomWS = 1 No stress
res2 <- c4photo(dat1$Qp,dat1$Tl,dat1$RH,StomWS=0.5)

## Plot comparing StomWS = 1 vs. 0.5 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('StomWS 1','StomWS 0.5')),
           lines=TRUE,col=c('blue','green'),lwd=2))


## Effect on Stomatal Conductance
## Plot comparing StomWS = 1 vs. 0.5 for a range of conditions
xyplot(res1$Gs + res2$Gs ~ Qp | factor(Tl) , data = dat1,
        type='l',col=c('blue','green'),lwd=2,
        ylab=expression(paste('Stomatal Conductance (mmol ',
          m^-2,' ',s^-1,')')),
        xlab=expression(paste('Quantum flux (',
          mu,mol,' ',m^-2,' ',s^-1,')')),
        key=list(text=list(c('StomWS 1','StomWS 0.5')),
           lines=TRUE,col=c('blue','green'),lwd=2))

## End(Not run)