The package currently supports three varieties of stomatal conductance models (Ball et al. 1987; Leuning 1995; Medlyn et al. 2011).
library(dplyr) library(photosynthesis) round_to_nearest = function(x, values) { sapply(x, function(y, values) { values[which.min(abs(y - values))] }, values = values) } # Read in data dat = system.file("extdata", "A_Ci_Q_data_1.csv", package = "photosynthesis") |> read.csv() |> # Convert RH to a proportion mutate( RH = RHcham / 100, PPFD = round_to_nearest(Qin, c(25, 50, 75, 100, 125, 375, 750, 1500)) ) |> rename(A_net = A, C_air = Ca, g_sw = gsw, VPD = VPDleaf) # Fit the Ball-Berry stomatal conductance models fit = fit_gs_model( data = filter(dat, PPFD == 750), model = c("BallBerry") ) # Look at BallBerry model summary: summary(fit[["BallBerry"]][["Model"]]) # Look at BallBerry parameters fit[["BallBerry"]][["Parameters"]] # Look at BallBerry plot # fit[["BallBerry"]][["Graph"]] # Fit many g_sw models fits = fit_many(dat, funct = fit_gs_model, group = "PPFD", progress = FALSE) # Look at the Medlyn_partial outputs at 750 PAR # Model summary summary(fits[["750"]][["Medlyn_partial"]][["Model"]]) # Model parameters fits[["750"]][["Medlyn_partial"]][["Parameters"]] # Graph # fits[["750"]][["Medlyn_partial"]][["Graph"]] # Compile parameter outputs for BallBerry model # Note that it's the first element for each PAR value # First compile list of BallBerry fits bbmods = compile_data(data = fits, output_type = "list", list_element = 1) # Now compile the parameters (2nd element) into a dataframe bbpars = compile_data(data = bbmods, output_type = "dataframe", list_element = 2) #Compile graphs graphs = compile_data(data = bbmods, output_type = "list", list_element = 3) # Look at 3rd graph # graphs[[3]]
Ball JT, Woodrow IE, Berry JA. 1987. A model predicting stomatal conductance and its contribution to the control of photosynthesis under different environmental conditions, in Progress in Photosynthesis Research, Proceedings of the VII International Congress on Photosynthesis, vol. 4, edited by I. Biggins, pp. 221–224, Martinus Nijhoff, Dordrecht, Netherlands.
Leuning R. 1995. A critical appraisal of a coupled stomatal-photosynthesis model for C3 plants. Plant, Cell & Environment 18:339-357.
Medlyn BE, Duursma RA, Eamus D, Ellsworth DS, Prentice IC, Barton CVM, Crous KY, Angelis PD, Freeman M, Wingate L. 2011. Reconciling the optimal and empirical approaches to modeling stomatal conductance. Global Change Biology 17:2134-2144.
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