c3photo: Simulates C3 photosynthesis

In BioCro: Simulation of Biomass Crops

Description

Simulates coupled assimilation and stomatal conductance based on Farquhar and Ball-Berry.

Usage

c3photo(Qp, Tl, RH, vcmax = 100, jmax = 180, Rd = 1.1, Catm = 380, 
    O2 = 210, b0 = 0.08, b1 = 5, theta = 0.7) 

Arguments

Qp	Quantum flux
Tl	Leaf temperature
RH	Relative humidity (fraction – 0-1)
vcmax	Maximum rate of carboxylation
jmax	Maximum rate of electron transport
Rd	Leaf dark respiration
Catm	Atmospheric carbon dioxide.
O2	Atmospheric Oxygen concentration (mmol/mol)
b0	Intercept for the Ball-Berry model
b1	Slope for the Ball-Berry model
theta	Curvature parameter

Details

The details of the model and equations are here: http://www.life.illinois.edu/plantbio/wimovac/leafgas.htm

Value

A list

Gs	Stomatal Conductance
Assim	CO2 Assimilation
Ci	Intercellular CO2

Author(s)

Fernando E. Miguez

References

Farquhar (1980) Ball-Berry (1987)

See Also

See Also Opc3photo

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,")")))

BioCro documentation built on May 2, 2019, 6:15 p.m.