read_psi_file_campbell: Function to import data from PSI FRRF using Doug Campbell...

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

Description

Imports a PSI FRRF data file generated by applying an FRRf induction/relaxation on top of a level of actinic light (which may = 0) and then again after a user defined dark period (ex. 1 s) to allow re-opening of PSII. Reads in data file, parses metadata, subtracts electronic background from fluorescence signal during light flashlets, splits columns into "light" and "dark" vectors, splits data by sti and str, calculates the actinic light level at each step.

Usage

read_psi_file_campbell(filename, calib_file = NA, dec = ".")

Arguments

filename	Path to the file to be imported
calib_file	Path to the calibration file to convert lamp voltage settings to photons. A^-2^ . s^-1^. If not provided the default is a calibration function from a Doug Campbell PSI FL3500 instrument. If you are not using his machine the parameters sigmaPSII, cumulative excitation and actinic PAR values associated to an individual machine will be wrongly calibrated.
dec	Decimal separator, default= "."

Value

Returns a list of five data frames and one numeric vector. 1 - all.data = raw data input; 2 - meta.data = acquisiton settings; flashlet_energy = the calculated flashlet energy from the calibration file; 3 - data.sti = induction only; 4 - data.str = re-opening only; 5 - measuring_steps = voltage and equivalent actinic PAR at each step.

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