Using plantecowrap"
In plantecowrap: Enhancing Capabilities of 'plantecophys'

Load Packages

library(plantecowrap)

Fit ACi Curves then fit temperature responses

#Read in data from package
data <- read.csv(system.file("extdata", "example_1.csv",
                             package = "plantecowrap"),
                 stringsAsFactors = FALSE)
#Fit ACi curves
fits <- fitacis2(data = data,
                 varnames = list(ALEAF = "A",
                                 Tleaf = "Tleaf",
                                 Ci = "Ci",
                                 PPFD = "PPFD",
                                 Rd = "Rd",
                                 Press = "Press"),
                 group1 = "Treat",
                 fitTPU = FALSE,
                 fitmethod = "bilinear",
                 gm25 = 10000, #Allows fitting on an ACi rather than ACc-basis
                 Egm = 0)

#Get ACi outputs
outputs <- acisummary(data, group1 = "Treat", fits = fits)

#Fit temperature response
#Note that this will return NA warnings because it runs through
#1000 sets of starting parameters for Vcmax and Jmax
tresp <- fit_topt_VJ(outputs)

#See parameters
tresp[[2]]

#See plot
tresp[[3]]

Fitting of multiple temperature responses

#Read in data from package
data2 <- read.csv(system.file("extdata", "example_2.csv",
                             package = "plantecowrap"),
                 stringsAsFactors = FALSE)
#Fit ACi curves
fits2 <- fitacis2(data = data2,
                 varnames = list(ALEAF = "A",
                                 Tleaf = "Tleaf",
                                 Ci = "Ci",
                                 PPFD = "PPFD",
                                 Rd = "Rd",
                                 Press = "Press"),
                 group1 = "Grouping",
                 fitTPU = FALSE,
                 fitmethod = "bilinear",
                 gm25 = 10000,
                 Egm = 0)

#Get ACi outputs
outputs <- acisummary(data2, group1 = "Grouping", fits = fits2)
#NOTE: if fitacis2 fails to fit a curve, some output elements will be "Failed"
#and need to be removed before acisummary() is run

#Split grouping variable
outputs <- separate(outputs, col = "ID", into = c("Treat", "Block"), sep = "_")

#Note that this will return NA warnings because it runs through
#1000 sets of starting parameters for Vcmax and Jmax. Some of
#these sets will not work and return the NA warning.
tresps <- fit_topt_VJs(data = outputs,
                       group = "Block")

#Get parameters
pars <- get_t_pars(tresps)

#Get graphs
graphs <- get_t_graphs(tresps)

#Print graphs
#To print to current working directory, set path = "./".
print_graphs(graphs,
             path = tempdir())

#View parameters
pars

#View graphs
#Note that the second graph is strange because A was simply multiplied by
#2 for the sample dataset
graphs[[1]]
graphs[[2]]