process_psi: Wrapper function to import data from PSI FRRf and fit...
In bmjesus/psifluo: Fits Kolber et al (1998) model to FL3500 data

Description Usage Arguments Value

View source: R/process_psi.R

This function will import a PSI Fluorwin output file and will attempt to fit FRRf induction/re-opening models to the dataset. It can process files generated with Doug Campbell's double FRRf protocol and with the PSI RLC wizard (not implemented yet).

process_psi(file_name, out_name = "results", sti_model = "all",
  str_model = "tau1", calib_file = NA, protocol = "campbell",
  turn_plots_off = FALSE, plot_matrix = FALSE, out_files = FALSE,
  out_pdf = FALSE, dec = ".", subset_time = 600)

`file_name`	Path to the file to be imported
`out_name`	Name the file to be exported with the results. Only works if the user selects out_files=TRUE.
`sti_model`	Parameters to fit to the induction 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.
`str_model`	Type of re-opening 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.
`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.
`protocol`	Type of protocol used to produce the PSI file. Currently only "campbell" is implemented.
`turn_plots_off`	Logical, plots off. Default = FALSE
`plot_matrix`	Logical, should plots be plotted to a plot matrix. Default = TRUE
`out_files`	Logical, should results (fitted parameters) be exported to a csv file. Default = FALSE
`out_pdf`	Logical, should plot be exported to a pdf file. Default = FALSE
`dec`	decimal separator, default= "."
`subset_time`	selects a subset of the re-opening dataset based on time (micro seconds) from the first point. To be used only with the tau1_subset model.

Returns a list with 3 elements. The first element (data) contains 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. The second element (sti_parameters) contains a data frame with fitted parameters for the induction step and respective SE, p-values.The third element (str_parameters) contains a data frame with fitted parameters for the re-opening step and respective SE, p-values.

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