## ----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)