Description Usage Arguments Details Value Note Author(s) References See Also Examples
Simulates coupled assimilation and stomatal conductance based on Farquhar and Ball-Berry.
1 2 | c3photo(Qp, Tl, RH, vcmax = 100, jmax = 180, Rd = 1.1,
Catm = 380, O2 = 210, b0 = 0.08, b1 = 5, theta = 0.7)
|
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 |
~~ If necessary, more details than the description above ~~
A list
~~further notes~~ ## Additional notes about assumptions
Fernando E. Miguez
Farquhar (1980) Ball-Berry (1987)
See Also Opc3photo
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 | ## 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,')')))
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