plantecowrap (version 1.0.4)

fit_topt_VJ: Fitting the temperature responses of Vcmax and Jmax

Description

Fitting the temperature responses of Vcmax and Jmax

Usage

fit_topt_VJ(
  data,
  varnames = list(Vcmax = "Vcmax", Jmax = "Jmax", Tleaf = "Tleaf"),
  title = NULL,
  limit_jmax = 1e+05,
  limit_vcmax = 1e+05,
  ...
)

Arguments

data

Dataframe containing Vcmax (maximum rubisco carboxylation capacity in umol m-2 s-1), Jmax (maximum photosynthetic electron transport to CO2 fixation in umol m-2 s-1), and Tleaf (leaf temperature in Celsius)

varnames

Variable names to account for different spellings of Vcmax, Jmax, and Tleaf.

title

Graph title, usually a group name

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(). See ?nlsLM for details.

Value

fit_topt_VJ fits the Topt modified Arrhenius function to Vcmax and Jmax data. Note that Hd may max out at 3000 kJ mol-1 for Jmax and 2000 kJ mol-1 for Vcmax. 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

# NOT RUN {
#Read in data
data <- read.csv(system.file("extdata", "example_1.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 = "Treat",
                 fitTPU = FALSE,
                 fitmethod = "bilinear",
                 gm25 = 10000,
                 Egm = 0)
#Extract coefficients
outputs <- acisummary(data, group1 = "Treat", fits = fits)
#Fit temperature response
tresp <- fit_topt_VJ(outputs)
#View plot
tresp[[3]]
# }