eemR and staRdom methods for fluorescence and absorbance indices

Calculates commonly used absorbance and fluorescence optical indices from eemlist and abslist objects using functions from the eemR and staRdom packages. Can incorporate sample metadata if provided.

Usage

eemR_indices(eemlist, abslist, cuvle = 1, qaqc_dir = NULL)

Arguments

eemlist: An eemlist object.
abslist: An abslist object.
cuvle: Cuvette (path) length in cm.
qaqc_dir: File path to the QAQC files generated with create_mdl() and create_std(). Default is a user-specific data directory rappdirs::user_data_dir().

Value

A list with two elements:

eem_index: a data.frame of all fluorescence indices. Each row corresponds to a single index for a sample.
abs_index: a data.frame of all absorbance indices. Each row corresponds to a single index for a sample.

Each data.frame contains the following columns:

sample_name: name of the sample from the EEM or absorbance list
meta_name: sample name from metadata if provided; otherwise same as sample_name
index: name of the index
value: calculated value of the index

Details

Absorbance indices (a254, a300, E2_E3, E4_E6, S275_295, S350_400, S300_700, SR) are calculated using staRdom::abs_parms().

Fluorescence indices are calculated using the following eemR functions:

Coble peaks (b, t, a, m, c): eemR::eem_coble_peaks()
fi (fluorescence index): eemR::eem_fluorescence_index()
hix (humification index): eemR::eem_humification_index() (use scale = TRUE for hix_scaled)
bix (biological index): eemR::eem_biological_index()

Examples

indices <- eemR_indices(
  eemlist = example_processed_eems,
  abslist = example_processed_abs,
  qaqc_dir = system.file("extdata", package = "eemanalyzeR")
)

# View fluorescence indices
head(indices$eem_index)
#>                           sample_name        meta_name index             value
#> 1                 B1S1ExampleBlankSEM     ExampleBlank     b            DATA01
#> 2                B1S2ExampleTeaStdSEM    ExampleTeaStd     b            DATA01
#> 3                B1S3ExampleSampleSEM    ExampleSample     b            DATA01
#> 4 ManualExampleTeaWaterfallPlotSample ManualExampleTea     b            DATA01
#> 5                 B1S1ExampleBlankSEM     ExampleBlank     t             MDL01
#> 6                B1S2ExampleTeaStdSEM    ExampleTeaStd     t 0.589498543201255

# View absorbance indices
head(indices$abs_index)
#>                        sample_name        meta_name index            value
#> 1              B1S1ExampleBlankABS     ExampleBlank  a254            MDL01
#> 2             B1S2ExampleTeaStdABS    ExampleTeaStd  a254 37.5817130707345
#> 3             B1S3ExampleSampleABS    ExampleSample  a254 18.5704030241273
#> 4 ManualExampleTeaAbsSpectraGraphs ManualExampleTea  a254 69.2896785319941
#> 5              B1S1ExampleBlankABS     ExampleBlank  a300            MDL01
#> 6             B1S2ExampleTeaStdABS    ExampleTeaStd  a300 20.2099169663529