staRdom is a package for R to analyse fluorescence and absorbance data of dissolved organic matter (DOM). It is possible to do the following steps:
* correcting excitation-emission-matrices (EEM, doi:10.1039/c3ay41160e, partly done with eemR)
* calculating fluorescence peaks and indices (done with eemR)
* biological index (bix, doi:10.1016/j.orggeochem.2009.03.002)
* so-called Coble-peaks (b, t, a, m, c, `r citet("10.1016/0304-4203(95)00062-3")`)
* fluorescence index (fi, doi:10.4319/lo.2001.46.1.0038)
* humification index (hix, doi:10.1021/es0155276)
* absorbance slope parameters (a254, a300, E2:E3, E4:E6, S275-295, S350-400, S300-700, SR, doi:10.4319/lo.2008.53.3.0955, doi:10.1016/j.marchem.2004.02.008)
* PARAFAC/CANDECOMP analysis can separate the components of the EEMs that can be linked to chemical components in DOM (doi:10.1039/c3ay41160e).
staRdom was developed and maintained at WasserCluster Lunz (http://www.wcl.ac.at/index.php/en/) and the University of Natural Resources and Life Sciences, Vienna (http://www.boku.ac.at/). Currently, the package is maintained as my personal project.
The analysis process was already discussed in other papers and tutorials. The aim of this package was to bring a familiar way of using PARAFAC analysis for DOM to the R platform. The offered functions follow the concept of doi:10.1039/c3ay41160e. Reading it is recommended and can help your understanding!
Changelog:
1.1.26 to 1.1.28
fixed example of eem_load_dreem due to problems on some computers reading UTF8 data
fixed deprecated functions in dplyr
added function do export data
updated links within the whole package
1.1.24 to 1.1.26
minor changes to class checks
bugfix in eem_import_dir
1.1.22 to 1.1.24
Fixed function eem_csv2
minor changes in warnings and errors
1.1.21 to 1.1.22
The default colour palette was changed to viridis to improve the readability for people with color vision deficiency.
The default ggplot theme of the plots was changed to theme_minimal()
splithalf_plot shows a legend to identify the subsets
1.1.20 to 1.1.21
fixed links in vignettes and help
1.1.19 to 1.1.20
eempf_res_analysis: function added to calculate residual metrics
Fixed example of eempf_report writing to home directory
Fixed generation of openfluor export demands email
1.1.18 to 1.1.19
PARAFAC models can be uploaded to openfluor.org directly
1.1.17 to 1.1.18
PARAFAC models are automatically scaled when exported to openfluor
1.1.16 to 1.1.17
corrected links in the manual
1.1.15 to 1.1.16
eempf_corcondia bug fixed
1.1.14 to 1.1.15
abs_blcor can handle single samples now
1.1.13 to 1.1.14
staRdom is fit for R 4.0 now
1.1.11 to 1.1.13
parafac_conv bug fixed
splithalf bug fixed
1.1.9 to 1.1.11
the use of colour palettes in plots was changed slightly to be more intuitive and consistent over all staRdom functions
1.1.8 to 1.1.9
changed citation system in vignettes: no internet connection necessary for knitting now
1.1.7 to 1.1.8
abs_parms: bug fixed, plain absorbance values were not multiplied by log(10)
1.1.5 to 1.1.7
eem_dilution: bug fixed
eem_smooth: bug fixed
1.1.4 to 1.1.5
eem_dilution: improved error behaviour
basic analysis: bug in contour plots corrected
eem_hitachi: throws an error instead of a warning if there is a problem
1.1.3 to 1.1.4
added error catcher to absorbance read to improve readability of errors.
1.1.2 to 1.1.3
corrected release date ;-)
1.1.1 to 1.1.2
eem_hitachi : added error catcher to provide more information in case of faulty files
eem_overview_plot: rows and columns of samples in a plot can be defined
eem_compare and eem_plot_comps: unequal wavelength slits do not show in the plots anymore
1.1.0 to 1.1.1
bug fixed: eempf4analysis now returnes loadings multiplied with normalisation factors
1.0.28 to 1.1.0
changes in examples
1.0.27 to 1.0.28
added information on paper comparing staRdom and drEEM
absorbance_read and abs_parms use multiple CPUs now
1.0.26 to 1.0.27
eem_smooth, eempf_ssc and eempf_ssccheck use multiple CPUs now
1.0.24 to 1.0.26
changes in vignettes
1.0.23 to 1.0.24
reduced package size by restructuring data
1.0.22 1.0.23
bugfix in eem_ife_correction
1.0.21 to 1.0.22
corrected broken links in vignettes
1.0.20 to 1.0.21
changes in vignettes
1.0.19 to 1.0.20
corrected an issue with absorption data
1.0.18 to 1.0.19
function eem_apply to apply any functions on EEMs
corrected wrong a254 and a300 were wrong when using absorption data
1.0.17 to 1.0.18
Minor issues to fulfill CRAN requirements
1.0.16 to 1.0.17
SSC included to measure the similarity between components
dec and sep recognition is possible with numbers in exponential format
SSCs between components of a model can be plotted
1.0.15 to 1.0.16
corrected reading single absorbance files
1.0.13 to 1.0.15
absorbance and absorption can be used for inner-filter effect correction
the desired number of converging models can be set optionally
1.0.12 to 1.0.13
adapted to work with eemR 1.0.1
added optional contours to plots
ensured nonnegative values with nonnegative constraints
corrected absorbance problem with the PARAFAC report
models and samples are plotted in same order as the list of models or samples
spectral correction is not limited to integer values anymore
solved issue with axis breaks
1.0.11 to 1.0.12
The PARAFAC tutorial was improved and extended again.
all examples are taken from drEEM now
eem_read_csv function to read EEM data from plain csv files
absorbance_read probably recognises csv separators more precisely now
eem_extend2largest adds NAs at wavelengths where data is present in any other sample in a set
eem_spectral_cor can do spectral corrections using one vector for emission and excitation each
eem_load_dreem loads the data from drEEM directly from the website into R
A_missing can be used to calculate A-modes from each combination of components now
eempf_excomp extract components from PARAFAC models to variables
eempf_bindxc bind extracted components into one set of components
1.0.10 to 1.0.11
absorbance parameters can be interpolated where wavelengths are missing
absorbance can be passed on as absorbance coefficient
1.0.9 to 1.0.10
corrected bug: functions not exported
PARAFAC models and components can have names
PARAFAC tutorial revised
exmaple data reduced again because of package size
eempf_varimp calculates the variable importance of the components
eempf_reorder can reorder the components in a PARAFAC model based on different criteria
1.0.8 to 1.0.9
Re-worked PARAFAC tutorial
abs_blcor does a baseline correction of absorbance data
abs_parms additionally calculates the spectral slope according to Loiselle, 2009
eem_setNA can remove defined data and optionally interpolate
additional methods for interpolation added
eem_matmult multiplies eem data with a certain matrix to cur out data ranges where you expect noise
eem_checkdata additionally checks the size of EEMs
abs_fit_slope does not produce errors (but a warning) if the absorbance wavelength is smaller than the desired slope limits.
absorbance_read is more reliable now and can deal with more formats
1.0.7 to 1.0.8
documentation was extended
reading absorbance data can determine decimal separator automatically
corrected broken dependency to multiway
1.0.6 to 1.0.7:
correction of sample normalisation
functions for merging diluted and undiluted samples
1.0.5 to 1.0.6:
absorbance_read: sep and dec are set automatically, location of files is saved
eem_checkdata: added functions to check imported data, checks sample names, missing data
eempf4analysis: create and optionally export table containing loadings from parafac, peaks, indices and absorbance slope parameters
eempf_eemqual: calculate model quality
eempf_report: create a report from a PARAFAC model and write out as html
1.0.3 to 1.0.5:
corrected severe bug in eem2array
corrected severe bug in norm_array
eem_parafac: bug in Windows multi core calculation corrected
A_missing computation time improved
maxlines computation time improved
help imporved on some topics
vaulty demo data sh corrected
added README