The package currently supports fitting light respiration according to the slope-intercept regression extension of the Laisk method (Laisk 1977; Walker & Ort 2015), the Kok method (Kok 1956), and the Yin modification of the Kok method (Yin et al. 2009, 2011)
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 your data
dat = system.file("extdata", "A_Ci_Q_data_1.csv", package = "photosynthesis") |>
read.csv() |>
mutate(group = round_to_nearest(CO2_s, values = c(50, 100, 200, 300, 410, 600, 820, 1200, 1600))) |>
rename(A_net = A, PPFD = Qin, phi_PSII = PhiPS2, C_i = Ci)
# Fit light respiration with Yin method
r_light = fit_r_light_yin(data = dat, PPFD_lower = 20, PPFD_upper = 250)
# Fit light respiration with Kok method
r_light = fit_r_light_kok(data = dat, PPFD_lower = 20, PPFD_upper = 150)
# Fit light respiration across groups with Yin method
r_lights = fit_many(
data = dat,
funct = fit_r_light_yin,
group = "group",
PPFD_lower = 20, PPFD_upper = 250,
progress = FALSE
)
#Fit the Walker-Ort method for GammaStar and light respiration
walker_ort = fit_r_light_WalkerOrt(dat)
# View model output
summary(walker_ort[[1]])
##
## Call:
## lm(formula = Intercept ~ Slope, data = coefs)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.36114 -0.10958 -0.05553 0.08166 0.62016
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -0.1526 0.1176 -1.297 0.224
## Slope -4.6004 0.4069 -11.307 5.1e-07 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.2513 on 10 degrees of freedom
## Multiple R-squared: 0.9275, Adjusted R-squared: 0.9202
## F-statistic: 127.8 on 1 and 10 DF, p-value: 5.103e-07
# View graph
# walker_ort[[2]]
# View coefficients
walker_ort[[3]]
## GammaStar r_light
## Slope 46.00427 -0.152643
Kok B. 1956. On the inhibition of photosynthesis by intense light. Biochimica et Biophysica Acta 21: 234–244
Laisk A. 1977. Kinetics of photosynthesis and photorespiration in C3 plants. Nauka, Moscow.
Walker BJ, Ort DR. 2015. Improved method for measuring the apparent CO2 photocompensation point resolves the impact of multiple internal conductances to CO2 to net gas exchange. Plant, Cell & Environment 38:2462- 2474
Yin X, Struik PC, Romero P, Harbinson J, Evers JB, van der Putten PEL, Vos J. 2009. Using combined measurements of gas exchange and chlorophyll fluorescence to estimate parameters of a biochemical C3 photosynthesis model: a critical appraisal and a new integrated approach applied to leaves in a wheat (Triticum aestivum) canopy. Plant, Cell & Environment 32:448-464
Yin X, Sun Z, Struik PC, Gu J. 2011. Evaluating a new method to estimate the rate of leaf respiration in the light by analysis of combined gas exchange and chlorophyll fluorescence measurements. Journal of Experimental Botany 62: 3489–3499