fit_topt_VJs: Fitting multiple temperature response curves

In plantecowrap: Enhancing Capabilities of 'plantecophys'

Description

Fitting multiple temperature response curves

Usage

fit_topt_VJs(
  data,
  group,
  varnames = list(Vcmax = "Vcmax", Jmax = "Jmax", Tleaf = "Tleaf"),
  limit_jmax = 1e+05,
  limit_vcmax = 1e+05,
  ...
)

Arguments

data	Dataframe with multiple temperature response curves for Vcmax (maximum rubisco carboxylation capacity in umol m-2 s-1) and Jmax (maximum photosynthetic electron transport to CO2 fixation in umol m-2 s-1).
group	Grouping variable to use, e.g. Plant ID
varnames	Variable names. Reassigns variable names to account for different spellings of Vcmax, Jmax, and Tleaf
limit_jmax	Upper limit to Jmax values for fitting. Defaults to 100,000 umol m-2 s-1 as this is the "nonsense output" from fitaci. Ensures that these points are not fit.
limit_vcmax	Upper limit to Vcmax values for fitting. Defaults to 100,000 umol m-2 s-1.
...	Arguments to be passed on to minpack.lm::nlsLM via fit_topt_VJ(). See ?nlsLM for details.

Value

fit_topt_VJs fits multiple Vcmax and Jmax temperature responses using the optimum temperature response model from Medlyn et al. 2002. REFERENCE Medlyn BE, Dreyer E, Ellsworth D, Forstreuter M, Harley PC, Kirschbaum MUF, Le Roux X, Montpied P, Strassemeyer J, Walcroft A, Wang K, Loutstau D. 2002. Temperature response of parameters of a biochemically based model of photosynthesis. II. A review of experimental data. Plant Cell Environ 25:1167-1179

Examples

#Read in data
data <- read.csv(system.file("extdata", "example_2.csv",
package = "plantecowrap"), stringsAsFactors = FALSE)
#Fit ACi Curves then fit temperature responses
fits <- fitacis2(data = data,
                 varnames = list(ALEAF = "A",
                                 Tleaf = "Tleaf",
                                 Ci = "Ci",
                                 PPFD = "PPFD",
                                 Rd = "Rd",
                                 Press = "Press"),
                 group1 = "Grouping",
                 fitTPU = FALSE,
                 fitmethod = "bilinear",
                 gm25 = 10000,
                 Egm = 0)
#Extract coefficients
outputs <- acisummary(data, group1 = "Grouping", fits = fits)
#Plot curve fits
for (i in 1:length(fits)) {
  plot(fits[[i]])
}
#Separate out grouping variable
outputs <- separate(outputs, col = "ID", c("Treat", "Block"), sep = "_")
#Fit the Topt model from Medlyn et al. 2002 for all individuals
#Output is a list of lists for each individual
#There is also a fit_topt_VJ for single temperature response
#fitting
out <- fit_topt_VJs(data = outputs,
                    group = "Block", #this grouping variable is for
                    #each individual
                    varnames = list(Vcmax = "Vcmax",
                                    Jmax = "Jmax",
                                    Tleaf = "Tleaf"),
                    limit_jmax = 100000,
                    limit_vcmax = 100000)
#Let's get the parameters out into a single data frame
pars <- get_t_pars(out)
#Let's get the graphs out into a list
#You can get a graph using: graph[1]
graphs <- get_t_graphs(out)

plantecowrap documentation built on April 14, 2020, 7:45 p.m.