fit_str: Fitting function for a FRRf re-opening curve

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

Description

This will fit a model to the re-opening 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_str(x, y, fo = NULL, fm = NULL, tau_model = "tau1",
  subset_time = 500, plots = TRUE)

Arguments

x	Vector with cumulative time in microseconds
y	Fluorescence vector
fo	Initial value for fo, if NULL then it defaults to the last point of the relaxation curve
fm	Initial value for fm, if NULL then it defaults to the first point of the relaxation curve
tau_model	Options: "tau1", "tau2", "tau3" and "tau1_subset" (the user selects a subset of the data starting from the first point of the re-opening curve). Default is tau1, fitting re-opening with a single phase exponential decay with lifetime of tau1.
subset_time	Amount of time to fit the tau1_subset model (default = 500 us)
plots	Turns on and off the plotting (TRUE, FALSE). Default is TRUE

Value

The function returns a list with: 1 - fitted parameters (list); 2 - fitted values (numeric vector); 3 - time in us (numeric vector)

Examples

fit_str(x = str_data$time, y = str_data$light_1,tau_model = 'tau1')

fit_str(x = str_data$time, y = str_data$light_1,tau_model = 'tau3')

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