Author: Joseph R. Stinziano and Christopher D. Muir
Date: 2024-11-24

# Fitting CO2 response curves

#### Joseph R. Stinziano and Christopher D. Muir

#### 2024-11-24

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]]

    ##   Num V_cmax V_cmax_se    J_max        J      J_se V_TPU V_TPU_se        R_d
    ## 6   0 62.797  2.176227 110.3051 103.9718 0.1847135  1000       NA -0.3470509
    ##      R_d_se     cost citransition1 citransition2 V_cmax_pts J_max_pts V_TPU_pts
    ## 6 0.3947545 1.063979      427.6839      1450.485          8         4         0
    ##   alpha alpha_g gamma_star25 Ea_gamma_star K_M25   Ea_K_M  g_mc25 Ea_g_mc Oconc
    ## 6  0.24       0        42.75         37830 718.4 65508.28 0.08701       0    21
    ##   theta_J
    ## 6    0.85

    # View graph
    fit[[2]]

    ## Warning: Removed 2 rows containing missing values or values outside the scale range
    ## (`geom_line()`).

    ## Warning: Removed 12 rows containing missing values or values outside the scale range
    ## (`geom_line()`).

    # View data with modeled parameters attached
    # fit[[3]]

    # Fit many curves
    fits = fit_many(
      data = dat,
      funct = fit_aci_response,
      group = "group",
      progress = FALSE
    )

    ## Warning: `fit_many()` was deprecated in photosynthesis 2.1.3.
    ## This warning is displayed once every 8 hours.
    ## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
    ## generated.

    # Print the parameters
    # First set of double parentheses selects an individual group value
    # Second set selects an element of the sublist
    fits[[3]][[1]]

    ##   Num  V_cmax V_cmax_se    J_max        J       J_se V_TPU V_TPU_se        R_d
    ## 6   0 8.94862 0.5509706 47.01527 16.63315 0.08692268  1000       NA -0.1565895
    ##      R_d_se      cost citransition1 citransition2 V_cmax_pts J_max_pts
    ## 6 0.1264438 0.1194886      441.2967      1442.493          8         4
    ##   V_TPU_pts alpha alpha_g gamma_star25 Ea_gamma_star K_M25   Ea_K_M  g_mc25
    ## 6         0  0.24       0        42.75         37830 718.4 65508.28 0.08701
    ##   Ea_g_mc Oconc theta_J
    ## 6       0    21    0.85

    # Print the graph
    fits[[3]][[2]]

    ## Warning: Removed 12 rows containing missing values or values outside the scale range
    ## (`geom_line()`).

    # 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)

# References

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.