---
title: "Fitting temperature response curves"
author: "Joseph R. Stinziano and Christopher D. Muir"
date: "`r Sys.Date()`"
output: rmarkdown::html_document
vignette: >
 %\VignetteIndexEntry{temperature-response}
 %\VignetteEngine{knitr::rmarkdown}
 %\VignetteEncoding{UTF-8}
---

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).

```{r, message = FALSE}

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
)
    
# 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"
)
    
# 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.