PARAFAC.cube.design: Combine EEMs produce by the Cary Eclipse fluorometer into a...

In RichardLaBrie/paRafac_correction: Corrects EEM all at once before using Matlab for PARAFAC

Combine EEMs produce by the Cary Eclipse fluorometer into a cube ready for PARAFAC analysis in Matlab

Description

This function reads any number of EEMs and produce a cube of EEMs. It enables the standardization into Raman Unit and instrument's corrections.

Usage

PARAFAC.cube.design(
  data.file = "data",
  excitation = c(220, 450, 5),
  emission = c(230, 600, 2),
  EMCOL = F,
  Subtract.Blank = T,
  RU = T,
  rm.corner = T,
  EmEx.cor = T,
  Inner = T,
  pathlength = 1,
  split = "_",
  skip = 1,
  dot.number = 1,
  NonNegativity = T,
  fluorometer = "Cary Eclipse",
  EEMskip = 1,
  rm.scat = T,
  zlim = c(0, 1),
  graph = F,
  RspectroAbs = F
)

Arguments

data.file	is the name of the main folder where CDOM, FDOM and nano folders are
excitation	is a vector of three variables of the scanning setup (min,max,interval). Default is c(220,450,5)
emission	is a vector of three variables of the scanning setup (min,max,interval). Default is c(230,600,2)
EMCOL	is a logical parameter indicating whether or not the emission are stored as column in the csv file. Default is FALSE.
RU	is a logical parameter to transform fluorescence intensities into Raman Unit at Ex = 350 nm. Default is TRUE.
rm.corner	is a logical parameter to set the bottom right corner values to 0
EmEx.cor	is a logical parameter to correct EEMs for emission and excitation corrections. Default is True. Emission and excitation file must be numerics only stored in csv file.
Inner	is a logical parameter to apply inner filter effect correction. Default is True
pathlength	is a real number indicating the length of the optical path in the spectrophotometer in cm. Default is 1
split	is the symbol used to separate each EEM when using a multicell holder
skip	is a parameter to determine how many lines will be skiped before the header in the absorbance files
dot.number	is the number of "." in the name of your EEMs file. This number includes the "." in ".csv"
NonNegativity	is a logical parameter to transform all negative fluorescence values into 0. Default is TRUE
fluorometer	is a paramater for the fluorometer model. Default is "Cary Eclipse". Other model supported: "Shimadzu"
EEMskip	is a parameter to skip lines in EEM file before data. Default is 1
rm.scat	is a logical parameter to remove Reyleigh and Raman scatterings.
zlim	is the intensity to plot the EEMs. Negative and values outside of scale bar will be white
graph	is a logical parameter to plot the Raman integration to transform data into RU. Default is false
RspectroAbs	is a logical parameter for the inner filter correction. When TRUE, CDOM data have been first treated by the RspectroAbs package developed by Simon Bélanger. Default is FASLE

RichardLaBrie/paRafac_correction documentation built on March 13, 2023, 2:11 p.m.