get_t_pars: Get temperature response parameters

In plantecowrap: Enhancing Capabilities of 'plantecophys'

Description

Get temperature response parameters

Usage

get_t_pars(data)

Arguments

data	List of data output from fit_topt_VJs

Value

get_t_pars returns temperature response parameters for Vcmax and Jmax from the group fitting process. Output is a dataframe.

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)

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