Ci data

fitComplete

R Documentation

fitComplete

Description

Fit A/Ci curves using forced values and dictated bounds. Returns a list with the fit, the graph, and the table.

Usage

fitComplete(
  data,
  name_assimilation = "A",
  name_ci = c("pCi", "Ci"),
  gammastar = 3.52,
  O2 = 21,
  pressure = 101,
  tleaf = 25,
  initialGuess = NA,
  forceValues = c(NA, NA, NA, NA, NA, NA, NA),
  bound_l = c(1, 1, 1, 0.001, 0.001, 0, 0),
  bound_h = c(1000, 1000, 1000, 30, 30, 1, 0.75),
  ignoreTPU = F,
  maxiter = 250,
  Kc = exp(35.9774 - (80.99/(0.008314 * (273.15 + tleaf)))),
  Ko = exp(12.3772 - (23.72/(0.008314 * (273.15 + tleaf))))
)

Arguments

`data`	The A/Ci data to be used
`name_assimilation`	The name given to the assimilation column in "data"
`name_ci`	Name given to the Ci column in "data"
`gammastar`	The Cc compensation point. Default: Tobacco.
`O2`	The oxygen concentration in parts per hundred.
`pressure`	Atmospheric pressure in kPa
`tleaf`	The leaf temperature, in celsius
`initialGuess`	Initial guesses for fitting. Will generate ok guesses automatically if not provided
`forceValues`	A vector of forced values in order: VcMax, J, TPU, gm, Rd, aG, aS
`bound_l`	The minimum values to be considered for each parameter
`bound_h`	the maximum value to be considered for each parameter
`ignoreTPU`	Whether to fit TPU or not. Leave false if you don't know what you're doing!
`maxiter`	Maximum number of iterations for fitting. Can run very slowly if you have a large dataset and high maxiter. Default 250
`Kc`	Michaelis-menten kinetic parameter for carboxylation
`Ko`	Michaelis-menten kinetic parameter for oxygenation