c4photo(Qp, Tl, RH, vmax = 39, alpha = 0.04, kparm = 0.7, theta = 0.83, beta = 0.93, Rd = 0.8, UPPERTEMP = 37.5, LOWERTEMP = 3, Catm = 380, b0 = 0.08, b1 = 3, StomWS = 1, ws = c("gs", "vmax"))
micro
mol m-2 s-1).micromol/mol).list structure with components
The mathematical model is based on Collatz et al (1992) (see References). Stomatal conductance is based on code provided by Joe Berry.
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.
## <strong>Not run</strong>: # ## 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 # # 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)) # ## <strong>End(Not run)</strong>
eC4photo