fit_sti: Fitting function for a FRRf induction curve

In bmjesus/psifluo: Fits Kolber et al (1998) model to FL3500 data

Description

This will fit a model to the induction phase using the equations of Zbigniew S. Kolber, Ondrej Prasil, Paul G. Falkowski (1998) Measurements of variable chlorophyll Fuorescence using fast repetition rate techniques: defining methodology and experimental protocols. Biochimica et Biophysica Acta, 1367: 88-106.

Usage

fit_sti(x, y, fo = NULL, fm = NULL, sigma.opt = 300, rho.opt = 0.1,
  fit_model = "all", plots = TRUE)

Arguments

x	Flashlet energy (photons . A^-2 . flashlet^-1) used to generate a x axis of cumulative energy by multiplying by flashlet count. A typical value from a flashlet calibration file of Doug Campbell's lab is 0.0002167971 (photons . A^-2 . flashlet^-1). This value is wrong if you are not using his machine and you should supply the correct value for your machine if you want to obtain correct sigma values (A^2 . PSII^-1).
y	Fluorescence data vector.
fo	Initial value for fo, default (NULL) is the 1st point of the fluorescence data vector y.
fm	Initial value for fm, default (NULL) is the average of the maximum 5 points of the fluorescence data vector y.
sigma.opt	Initial value for sigma, default = 300 A^2 PSII^-1.
rho.opt	Initial value for rho excitonic connectivity among PSII units, default = 0.1.
fit_model	How many parameters to fit to the curve. Default is "all". Options are: "all", "sigma_rho" and "sigma". "All" - fo, fm, sigma and rho are fitted; "sigma_rho" - sigma and rho are fitted, fo and fm are fixed at user-defined levels, defaults are fo = 1st point of the fluorescence data vector y, fm = average of the maximum 5 points of the fluorescence data vector y; "sigma" - fo, fm and rho are fixed, only sigma is fitted.
plots	Turns on and off plotting of data and fitted curves (TRUE, FALSE). Default is TRUE.

Value

The function returns a list with: 1- fitted parameters and respective SE, p-values (list); 2 - flashlet energy (single element numeric vector); 3- fitted values (numeric vector); 4 - cumulative energy (numeric vector).

Examples

fit_sti(x = 0.0002167971, y = sti_data$light_1,fit_model = 'all')

fit_sti(x = 0.0002167971, y = sti_data$light_1,fit_model = 'sigma_rho')

bmjesus/psifluo documentation built on Aug. 27, 2020, 1:47 a.m.