Fitting temperature response curves

This package provides support for multiple temperature response functions (Arrhenius 1915; Medlyn et al. 2002; Kruse & Adams. 2006; Heskel et al. 2016; Liang et al. 2018).

library(dplyr)
library(photosynthesis)
library(tidyr)

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_T_data.csv", package = "photosynthesis") |>
  read.csv() |>
  mutate(
    group = as.factor(round_to_nearest(Tleaf, seq(17.5, 40, by = 2.5))),
    # Convert data temperature to K
    T_leaf = Tleaf + 273.15
  ) %>%
  # Calculate mean temperature for group so temperature
  full_join(
    . |>
      group_by(ID, group) |>
      summarize(Curve_Tleaf = round(mean(Tleaf), 1), .groups = "drop"),
    by = c("ID", "group")
  ) |>
  # Create ID column to curve fit by ID and temperature
  mutate(ID2 = paste(ID, Curve_Tleaf, sep = "_")) |>
  rename(A_net = A, C_i = Ci, PPFD = Qin)
   
# Fit many CO2 response curves
fits = fit_many(
  data = dat,
  group = "ID2",
  funct = fit_aci_response,
  alphag = 0,
  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.

# Extract ACi parameters
pars = compile_data(fits, output_type = "dataframe", list_element = 1)
    
# Extract ACi graphs
graphs = compile_data(fits, output_type = "list", list_element = 2)
    
# Parse the ID variable
pars = separate(pars, col = "ID", into = c("ID", "Curve_Tleaf"), sep = "_") |>
  mutate(
    # Make sure curve leaf temperature is numeric and convert to K
    T_leaf = as.numeric(Curve_Tleaf) + 273.15
  )
    
fit = fit_t_response(
  data = filter(pars, ID == "S2"),
  varnames = list(Par = "V_cmax", T_leaf = "T_leaf"),
  setvar = "Hd"
)

## Warning in fit_t_response(data = filter(pars, ID == "S2"), varnames = list(Par
## = "V_cmax", : NAs introduced by coercion

## Warning in fit_t_response(data = filter(pars, ID == "S2"), varnames = list(Par
## = "V_cmax", : NAs introduced by coercion
## Warning in fit_t_response(data = filter(pars, ID == "S2"), varnames = list(Par
## = "V_cmax", : NAs introduced by coercion
## Warning in fit_t_response(data = filter(pars, ID == "S2"), varnames = list(Par
## = "V_cmax", : NAs introduced by coercion
## Warning in fit_t_response(data = filter(pars, ID == "S2"), varnames = list(Par
## = "V_cmax", : NAs introduced by coercion
## Warning in fit_t_response(data = filter(pars, ID == "S2"), varnames = list(Par
## = "V_cmax", : NAs introduced by coercion
## Warning in fit_t_response(data = filter(pars, ID == "S2"), varnames = list(Par
## = "V_cmax", : NAs introduced by coercion
## Warning in fit_t_response(data = filter(pars, ID == "S2"), varnames = list(Par
## = "V_cmax", : NAs introduced by coercion
## Warning in fit_t_response(data = filter(pars, ID == "S2"), varnames = list(Par
## = "V_cmax", : NAs introduced by coercion

# Graphs
# fit[["Arrhenius"]][["Graph"]]
# fit[["Heskel"]][["Graph"]]
# fit[["Kruse"]][["Graph"]]
# fit[["Medlyn"]][["Graph"]]
# fit[["MMRT"]][["Graph"]]
# fit[["Quadratic"]][["Graph"]]
# fit[["Topt"]][["Graph"]]

References

Arrhenius S. 1915. Quantitative laws in biological chemistry. Bell.

Heskel MA, O’Sullivan OS, Reich PB, Tjoelker MG, Weerasinghe LK, Penillard A, Egerton JJG, Creek D, Bloomfield KJ, Xiang J, Sinca F, Stangl ZR, la Torre AM, Griffin KL, Huntingford C, Hurry V, Meir P, Turnbull MH, Atkin OK. 2016. Convergence in the temperature response of leaf respiration across biomes and plant functional types. PNAS 113:3832-3837

Kruse J, Adams MA. 2008. Three parameters comprehensively describe the temperature response of respiratory oxygen reduction. Plant, Cell & Environment 31:954-967

Liang LL, Arcus VL, Heskel MA, O’Sullivan OS, Weerasinghe LK, Creek D, Egerton JJG, Tjoelker MG, Atkin OK, Schipper LA. 2018. Macromolecular rate theory (MMRT) provides a thermodynamics rationale to underpin the convergent temperature response in plant leaf respiration. Global Change Biology 24:1538-1547

Medlyn BE, Dreyer E, Ellsworth D, Forstreuter M, Harley PC, Kirschbaum MUF, Le Roux X, Montpied P, Strassemeyer J, Walcroft A, Wang K, Loutstau D. 2002. Temperature response of parameters of a biochemically based model of photosynthesis. II. A review of experimental data. Plant, Cell & Environment 25:1167-1179.

Joseph R. Stinziano and Christopher D. Muir

2024-11-23

References