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

The package currently supports three varieties of stomatal conductance models
(Ball *et al.* 1987; Leuning 1995; Medlyn *et al.* 2011).

```{r, message = FALSE}

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]]
```

# References

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.