Takes raw EEMs and absorbance data from Aqualog, returns cleaned, processed data Combines all the 'fewsdom' functions to make one function to process samples.

Usage

run_eems(
  prjpath,
  meta_name,
  get_doc = F,
  doc_file,
  doc_sheet,
  doc_column = 7,
  name_column = 4,
  nskip = 3,
  doc_delim = "-",
  meta_sheet = "log",
  site_loc = c(1, 7),
  process_file = T,
  ...
)

Arguments

prjpath: path to folder with raw samples
meta_name: the file name of the metadata with the extension
get_doc: logical, if TRUE will use 'get_doc' function to match DOC data to metadata samples, only required if get_doc is TRUE
doc_file: a string of the file path of the DOC file, can be .xlsx or .csv, only required if get_doc is TRUE
doc_sheet: a string of the sheet name of the DOC results, only required if the DOC file is an .xlsx file, only required if get_doc is TRUE
doc_column: a numeric indicating which column the DOC results are stored in in the DOC file, only required if get_doc is TRUE
name_column: a numeric indicating which column the sample/site names are stored in the DOC file, only required if get_doc is TRUE
nskip: a numeric indicating a number of lines to skip when reading in the DOC file, optional, only required if get_doc is TRUE
doc_delim: a string indicating the separation between site name and other identifiers in the DOC data, it will only keep the first piece, only required if get_doc is TRUE
meta_sheet: a string of the metadata sheet name, only required if the metadata file is an .xlsx file
site_loc: a vector indicating the start and end of the site name in the metadata data identifier
process_file: logical, if TRUE it will put a text file in the processed data folder named 'processing_tracking'
...: additional arguments passed to the 'get_doc', 'clean_files', 'abs_preprocess', 'load_eems', 'eem_process', 'plot_eems', 'get_indices', 'save_eems' functions

Value

saves processed EEMs as .csv and .rds files, absorbance as .csv and .rds, and metadata as .csv creates plots for each sample and calculates indices.

Details

The following steps are chosen by default: -DOC is added to the metadata and the file is overwritten

-The file directory is created, raw files are zipped

-A process file is created, The instrument blank is subtracted from the samples, raman scattering is removed and interpolated, rayleigh scattering is removed but not interpolated, widths are determined automatically, samples are corrected for inner filter effects, raman normalized, and normalized for DOC, excitation is clipped from 247 to 450 nm, emission is clipped from 247 to 550 nm

-Sample are plotted individually and a summary plot using the parula color palette with descriptions for the plot titles, the peaks are not annotated on the plot. Plots are created for DOC normalized data (_DOC), and for non normalized data.

-Fluorescence indices are reported for data that has and hasn't been DOC normalized, sample are reported in rows.

If you want to change these defaults add the appropriate arguments into the function to change the defaults for the other functions.