Tools for Pre-Processing Emission-Excitation-Matrix (EEM) Fluorescence Data

Provides various tools for preprocessing Emission-Excitation-Matrix (EEM) for Parallel Factor Analysis (PARAFAC). Different methods are also provided to calculate common metrics such as humification index and fluorescence index.


eemR

The eemR package implements various functions used calculate metrics from excitation-emission matrix (EEM) as well as to preform pre-processing corrections before PARAFAC analysis.

The lastest release of the package from CRAN can be installed with:

install.packages("eemR")

The lastest development version of the package can be installed with:

devtools::install_github("PMassicotte/eemR")

A detailed vignette presenting the package which can be viewed using:

vignette(topic = "introduction", package = "eemR")

At the moment, the following EEM types are supported:

  • Cary Eclipse .csv files

  • Aqualog .dat files

  • Shimadzu .TXT files

EEM can be read using the eem_read() function. Please fill an issue if you have other file formats you would like to add to the package.

At the moment I need files from:

  • FluoromaxIII

  • Perkin elmer

  • Hitachi

News

eemR 0.1.4

  • eem_extract() is now more intuitive to use. remove argument has been replace by keep. If TRUE, the specified samples will be returned. If FALSE, they will be removed (#37).

  • eem_cut() now removes specified wavelenghts instead of keeping them.

  • eem_cut() gains an argument fill_with_na. If TRUE fluorescence at specified wavelengths will be replaced with NA instead of being removed.

  • File structure is now kept when performing inner-filter effect correction (#35).

  • Now using viridis space colors for plotting EEMs instead of color jet.

  • eem_remove_scattering() no longer tolower absorbance names and will assume that the provided absorbance spectra match exactly EEM's names.

  • Fixing a bug that prevented the interactive plot to work properly.

  • summary(x) and print(x) now return a data frame containing summarized information on EEMs contained in x. See ?summary.eemlist.

  • eem_raman_normalisation() and eem_remove_blank() will average blank EEMs if more than one are provided or found in the folder (#23).

  • eem_raman_normalisation(), eem_remove_blank() and eem_inner_filter_effect() will now verify if the correction has been already performed. If so, an unmodified EEM will be returned.

  • eem_raman_normalisation() now interpolates blank EEM to ensure that em at 350 and excitation between 371 and 428 exist (#31).

  • eem_remove_blank() and eem_raman_normalisation() will now keep blank samples when automatic correction is used. When automatic correction is used, the untransformed blank sample will be keep in the list.

  • An error will now occur if trying to perform blank correction after Raman normalization.

eemR 0.1.3

  • Interactive plot using a simple shiny app. Using plot(eems, interactive = TRUE) will lunch a shiny app that allows to interactively browse EEMs contained in eems.

  • A vignette has been added to the package whic can be viewed using vignette(topic = "introduction", package = "eemR").

  • An error will occur if one try to do raman normalization on a blank where scattering bands have been removed.

  • eem_sample_names() has been replaced by eem_names().

  • Reading Aqualog files is now ~20% faster (#26).

  • plot() gains an argument show_peaks = TRUE/FALSE which can be used to display most common fluorescence peaks used in the literature.

  • eem_remove_blank() and eem_raman_normalisation() can now try to implicitly use a blank eem from a eemlist object (#20). If blank is omitted (blank = NA), the functions will try to extract the blank from the eemlist object. This is done by looking for sample names containing one of these complete or partial strings (ignoring case): - "nano" - "miliq" - "milliq" - "mq" - "blank"

Consider the following example where there are two folders that could represent scans performed on two different days scans_day_1 and scans_day_2. In each folder there are three samples and one blank files. In that context, eem_remove_blank() will use the blank nano.csv from sample1.csv, sample2.csv and sample3.csv. The same strategy will be used for files in folder scans_day_2 but with blank named blank.csv.

inst/extdata/cary/
├── scans_day_1
│   ├── nano.csv
│   ├── sample1.csv
│   ├── sample2.csv
│   └── sample3.csv
└── scans_day_2
    ├── blank.csv
    └── s1.csv
  • eem_extract() has now an argument verbose (default = FALSE) that determine if the names of removed or extracted eems should be printed on screen.

  • Implemented the generic print() method which calls summary().

  • Added tests to the packages to verify metrics.

  • Now better estimate the number of columns to read in Cary Eclipse files (#27). This also makes reading much faster.

eemR 0.1.2

  • Sample names are now exported when using the eem_export_matlab() function.

  • New function eem_bind() implemented to merge objects of class eem and eemlist.

  • Reading EEMs should be ~ 50% faster.

  • New function eem_sample_names() implemented.

    • eem_sample_names(eem) returns a vector containing the sample names of all EEMs.
    • eem_sample_names(eem) <- c(...) sets the sample names of all EEMs.
  • eem_extract() has now an argument ignore_case (#10) to specify if the regular expression search should ignore sample name case (TRUE) or not (FALSE).

  • Sample names (i.e. file names) are now verified with make.names() (#15).

  • Various improvements in documentation.

eemR 0.1.1

  • Fixing minimal R version to run the package (R >= 3.2.1)

eemR 0.1.0

  • First version of eemR

Reference manual

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install.packages("eemR")

0.1.5 by Philippe Massicotte, 4 months ago


https://github.com/PMassicotte/eemR


Report a bug at https://github.com/PMassicotte/eemR/issues


Browse source code at https://github.com/cran/eemR


Authors: Philippe Massicotte [aut, cre]


Documentation:   PDF Manual  


GPL (>= 2) license


Imports stringr, dplyr, R.matlab, pracma, readr, stats, rlist, viridis

Suggests cdom, magrittr, testthat, knitr, rmarkdown, ggplot2, plot3D, extrafont, tidyr, shiny, DT


Suggested by cdom.


See at CRAN