NEWS.md

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

eemR 1.0.1

• Fixing file location that was not following when creating eems (#52).

eemR 1.0.0

Major changes

eemR can use user-defined function to import eems data. A new argument import_function in the eem_read() function can be used to provide a custom functio to read a speficic eem file format.

## Bracking changes

Because of the major change of eem_read(), existing code will brake. The user still can uses the old importing functions by specifying the spectrofluorometer to use as follows:

• eem_read(file, import_function = "cary"
• eem_read(file, import_function = "aqualog"
• eem_read(file, import_function = "shimadzu"
• eem_read(file, import_function = "fluoromax4"

New features

• New function eem_peaks() to extract user-defined fluorescence peaks (#42).

eemR 0.1.5

• Improved plot visualization to the same look and feel as those produced in Matlab with DrEEM.

• Use file name as is for the name of the eem.

• Reading Cary Eclipse files is more robust at detecting correct excitation wavelengths.

• eemR can now read Fluoromax-4 files (#40).

• eem_cut() gains a logical argument exact. If TRUE, only wavelengths matching em and/or ex will be removed. If FALSE, all wavelengths in the range of em and/or ex will be removed.

• Taking into account cuvette size to calculate the 1.5 threshold proposed by Kothawala when correcting for IFE.

• Inner-filter effect correction factors are now corrected correctly. Because fluorescence is assumed to be measured in 1 cm cuvette, absorbance is now expressed per centimeter.

• Better guessing the number of columns of the fluorescence matrix produced by Cary Eclipse software.

• Fixed many typos.

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 wavelengths 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 which 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

eemR documentation built on June 27, 2019, 5:08 p.m.