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co2-response.Rmd
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co2-response.Rmd
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---
title: "Fitting CO2 response curves"
author: "Joseph R. Stinziano and Christopher D. Muir"
date: "`r Sys.Date()`"
output: rmarkdown::html_document
vignette: >
%\VignetteIndexEntry{co2-response}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
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).
```{r, message = FALSE}
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)
```
# 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.