Process EEMs samples — eem_proccess • fewsdom

Takes EEMs data with blanks and absorbance data and will perform processing steps including blank subtraction, removing raman and rayleigh scattering, dilution correction, removing inner filtering effects, raman normalization.

Usage

eem_proccess(
  prjpath,
  eemlist,
  blanklist,
  abs,
  meta,
  process_file = T,
  replace_blank = F,
  raman = T,
  rayleigh = T,
  IFE = T,
  raman_norm = T,
  dilute = T,
  ex_clip = c(247, 450),
  em_clip = c(247, 600),
  raman_width = "auto",
  raman_mask = c(8, 8, 1.5, 1.5),
  rayleigh_width = "manual",
  rayleigh_mask = c(20, 10, 10, 10),
  ...
)

Arguments

prjpath: the file path of the main file directory where data is located
eemlist: object of class eem or eemlist containing EEMs samples
blanklist: object of class eem or eemlist containing the blanks for the EEMs samples should be the same length as eem
abs: dataframe containing absorbance data corresponding to the EEMs samples
meta: dataframe of metadata containing unique ID's, integration time, dilutions, and raman area for each sample, see example metadata for format
process_file: logical, if TRUE it will put a text file in the processed data folder named 'processing_tracking'
replace_blank: logical, if TRUE it will find the first sample labeled "blank" or "blk" and use that for blank subtraction, use when instrument blank has errors
raman: logical, if TRUE will use 'raman' function to remove raman scattering
rayleigh: logical, if TRUE will use 'rayleigh' function to remove rayleigh scattering
IFE: logical, if TRUE will use absorbance data to remove inner filter effects
raman_norm: logical, if TRUE will normalize EEMs to raman unit area
dilute: logical, if TRUE will correct for dilution factors given in metadata table
ex_clip: vector of length two with the excitation wavelengths to clip the EEMs to
em_clip: vector of length two with the emission wavelengths to clip the EEMs to
raman_width: either "auto" or "manual". If auto is chosen cutting widths will be found using the 'find_cut_width' function
raman_mask: a vector of length 4 specifying the width of the raman line to cut, numbers 1:2 are width above and below first order line, numbers 3:4 are width above and below second order line, since you cannot use the auto method for second order raman this must be specified
rayleigh_width: either "auto" or "manual", if auto is chosen cutting widths will be found using the 'find_cut_width' function
rayleigh_mask: optional if auto width method is used, a vector of length 4 specifying the width of the rayleigh line to cut, numbers 1:2 are width above and below first order line, numbers 3:4 are width above and below second order line
...: arguments passed on to scattering functions 'raman' and 'rayleigh'

Value

an list where the first object is of class eemlist with processed EEMs samples. The second object is a dataframe with the processes absorbance data. If a process file is given, a file will be created in the processes folder of the file directory

Examples

if (FALSE) {
data_process <- eem_proccess(prjpath=prjpath, eemlist=X, blanklist=X_blk, abs=Sabs,
process_file=process_file, meta=meta)

X_clean <- data_process[[1]]
abs_clean <- data_process[[2]]}