This package currently implements a Gu-type fitting procedure for CO2 response curves similar to the Duursma (2015) implementation. There is ongoing work to implement a full Gu-type method whereby mesophyll conductance, Km, and GammaStar could all be fit (Gu et al. 2010).
library(dplyr) library(photosynthesis) # Read in your data dat = system.file("extdata", "A_Ci_Q_data_1.csv", package = "photosynthesis") |> read.csv() |> mutate( # Set grouping variable group = as.factor(round(Qin, digits = 0)), # Convert data temperature to K T_leaf = Tleaf + 273.15 ) |> rename(A_net = A, PPFD = Qin, C_i = Ci) # Fit ACi curve. # Note that we are filtering the data.frame to fit for a single light value fit = fit_aci_response(filter(dat, group == 1500)) # View fitted parameters fit[[1]] # View graph fit[[2]] # View data with modeled parameters attached # fit[[3]] # Fit many curves fits = fit_many( data = dat, funct = fit_aci_response, group = "group", progress = FALSE ) # Print the parameters # First set of double parentheses selects an individual group value # Second set selects an element of the sublist fits[[3]][[1]] # Print the graph fits[[3]][[2]] # Compile graphs into a list for plotting fits_graphs = compile_data(fits, list_element = 2) # Print graphs to jpeg # print_graphs(data = fits_graphs, path = tempdir(), output_type = "jpeg") # Compile parameters into data.frame for analysis fits_pars = compile_data(fits, output_type = "dataframe", list_element = 1)
Duursma R. 2015. Plantecophys - an R package for analysing and modeling leaf gas exchange data. PLoS ONE 10:e0143346
Gu L, Pallardy SG, Tu K, Law BE, Wullschleger SD. 2010. Reliable estimation of biochemical parameters from C3 leaf photosynthesis-intercellular carbon dioxide response curves. Plant, Cell & Environment 33:1582-1874.
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