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## ---- echo = TRUE, eval = FALSE-----------------------------------------------
#
# #Read in your data
# #Note that this data is coming from data supplied by the package
# #hence the complicated argument in read.csv()
# #This dataset is a CO2 by light response curve for a single sunflower
# data <- read.csv(system.file("extdata", "A_Ci_Q_data_1.csv",
# package = "photosynthesis"))
#
# #Define a grouping factor based on light intensity to split the ACi
# #curves
# data$Q_2 <- as.factor((round(data$Qin, digits = 0)))
#
# #Convert data temperature to K
# data$T_leaf <- data$Tleaf + 273.15
#
# #Run a sensitivity analysis on GammaStar and mesophyll conductance
# #at 25 Celsius for one individual curve
# pars <- analyze_sensitivity(data = data[data$Q_2 == 1500, ],
# funct = fit_aci_response,
# varnames = list(A_net = "A",
# T_leaf = "T_leaf",
# C_i = "Ci",
# PPFD = "Qin"),
# useg_mct = TRUE,
# test1 = "gamma_star25",
# element_out = 1,
# test2 = "g_mc25",
# fitTPU = TRUE,
# Ea_gamma_star = 0,
# Ea_g_mc = 0,
# values1 = seq(from = 20,
# to = 60,
# by = 4),
# values2 = seq(from = 0.2,
# to = 2,
# by = 0.1))
#
# #Compute measures of sensitivity
# par2 <- compute_sensitivity(data = pars,
# varnames = list(Par = "V_cmax",
# test1 = "gamma_star25",
# test2 = "g_mc25"),
# test1_ref = 40,
# test2_ref = 1)
# #Plot sensitivity
# ggplot(par2, aes(y = CE_gamma_star25, x = CE_g_mc25, colour = V_cmax))+
# labs(x = expression(g_mc[25]~"Control Coefficient"),
# y = expression(Gamma[25]~"Control Coefficient")) +
# geom_point() +
# theme_bw()
#
# ggplot(par2, aes(y = CE_gamma_star25, x = V_cmax, colour = gamma_star25))+
# geom_point() +
# theme_bw()
# #Note that in this case a missing point appears due to an infinity
# #Can also plot sensitivity measures in 2 dimensions
# ggplot(par2, aes(x = gamma_star25, y = g_mc25, z = CE_gamma_star25))+
# geom_tile(aes(fill = CE_gamma_star25)) +
# labs(x = expression(Gamma*"*"[25]~"("*mu*mol~mol^{-1}*")"),
# y = expression(g[m][25]~"("*mu*mol~m^{-2}~s^{-1}~Pa^{-1}*")"))+
# scale_fill_distiller(palette = "Greys") +
# geom_contour(colour = "Black", size = 1) +
# theme_bw()
#
# plot(PE_gamma_star25 ~ gamma_star25, par2)
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