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

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Provides various tools to calculate EEM fluorescence metrics and preprocess EEM for PARAFAC analysis.

Author
Philippe Massicotte [aut, cre]
Date of publication
2016-08-29 14:16:11
Maintainer
Philippe Massicotte <pm@bios.au.dk>
License
GPL (>= 2)
Version
0.1.4
URLs

View on CRAN

Man pages

absorbance
CDOM absorbance data.
eem
eem constructor
eem_bind
Bind eem or eemlist
eem_biological_index
Calculate the biological fluorescence index (BIX)
eem_coble_peaks
Extract fluorescence peaks
eem_cut
Cut emission and/or excitation wavelengths from EEMs
eem_export_matlab
Export EEMs to Matlab
eem_extract
Extract EEM samples
eem_extract_blank
Extract blank EEM
eem_fluorescence_index
Calculate the fluorescence index (FI)
eem_humification_index
Calculate the fluorescence humification index (HIX)
eem_inner_filter_effect
Inner-filter effect correction
eem_names
The names of an eem or eemlist objects
eem_names-set
Set the sample names of an eem or eemlist objects
eem_raman_normalisation
Fluorescence Intensity Calibration Using the Raman Scatter...
eem_read
Read excitation-emission fluorecence matrix (eem)
eem_remove_blank
Blank correction
eem_remove_scattering
Remove Raman and Rayleigh scattering
eem_set_wavelengths
Set Excitation and/or Emission wavelengths
plot.eemlist
Surface plot of eem
print.eemlist
Display summary of an eemlist object
summary.eem
Display summary of an eem object
summary.eemlist
Display summary of an eemlist object

Files in this package

eemR
eemR/inst
eemR/inst/extdata
eemR/inst/extdata/cary
eemR/inst/extdata/cary/scans_day_2
eemR/inst/extdata/cary/scans_day_2/blank.csv
eemR/inst/extdata/cary/scans_day_2/s1.csv
eemR/inst/extdata/cary/scans_day_1
eemR/inst/extdata/cary/scans_day_1/nano.csv
eemR/inst/extdata/cary/scans_day_1/sample1.csv
eemR/inst/extdata/cary/scans_day_1/sample3.csv
eemR/inst/extdata/cary/scans_day_1/sample2.csv
eemR/inst/extdata/shimadzu
eemR/inst/extdata/shimadzu/shimadzu.TXT
eemR/inst/extdata/aqualog
eemR/inst/extdata/aqualog/sample4.dat
eemR/inst/doc
eemR/inst/doc/eemR_intro.R
eemR/inst/doc/eemR_intro.html
eemR/inst/doc/parafac.html
eemR/inst/doc/eemR_intro.Rmd
eemR/inst/doc/introduction.R
eemR/inst/doc/parafac.R
eemR/inst/doc/introduction.html
eemR/inst/doc/parafac.Rmd
eemR/inst/doc/introduction.Rmd
eemR/tests
eemR/tests/testthat.R
eemR/tests/testthat
eemR/tests/testthat/test-metrics.R
eemR/tests/testthat/test-blank-correction.R
eemR/NAMESPACE
eemR/NEWS.md
eemR/data
eemR/data/absorbance.RData
eemR/R
eemR/R/eem_correction.R
eemR/R/eem_metrics.R
eemR/R/eem_utils.R
eemR/R/eem_export.R
eemR/R/eem_read.R
eemR/R/absorbance.R
eemR/vignettes
eemR/vignettes/blank.rda
eemR/vignettes/ife.rda
eemR/vignettes/biblio.bib
eemR/vignettes/introduction.Rmd
eemR/README.md
eemR/MD5
eemR/build
eemR/build/vignette.rds
eemR/DESCRIPTION
eemR/man
eemR/man/eem_biological_index.Rd
eemR/man/eem_names-set.Rd
eemR/man/eem_remove_scattering.Rd
eemR/man/eem_coble_peaks.Rd
eemR/man/eem_inner_filter_effect.Rd
eemR/man/summary.eem.Rd
eemR/man/eem_remove_blank.Rd
eemR/man/eem_extract.Rd
eemR/man/eem.Rd
eemR/man/eem_raman_normalisation.Rd
eemR/man/print.eemlist.Rd
eemR/man/eem_names.Rd
eemR/man/eem_fluorescence_index.Rd
eemR/man/eem_humification_index.Rd
eemR/man/plot.eemlist.Rd
eemR/man/eem_cut.Rd
eemR/man/summary.eemlist.Rd
eemR/man/eem_bind.Rd
eemR/man/eem_read.Rd
eemR/man/eem_export_matlab.Rd
eemR/man/eem_extract_blank.Rd
eemR/man/absorbance.Rd
eemR/man/eem_set_wavelengths.Rd