abs_parms: Calculating slopes and slope ratios of a data frame of...
In jakehosen/stardom_aqualog: PARAFAC Analysis of EEMs from DOM

Description Usage Arguments Details Value References Examples

Calculating slopes and slope ratios of a data frame of absorbance data.

abs_parms(abs_data, cuvle, unit = "absorbance", add_as = NULL,
  limits = list(c(275, 295), c(350, 400), c(300, 700)),
  l_ref = list(275, 350, 300), S = TRUE, lref = FALSE, p = FALSE,
  model = FALSE, Sint = FALSE, interval = 21, r2threshold = 0.8,
  cores = parallel::detectCores(logical = FALSE), verbose = FALSE)

`abs_data`	data frame containing absorbance data.
`cuvle`	path length in cm
`unit`	unit of absorbance data: if "absorbance", absorbance data is multiplied by log(10) = 2.303 for slope calculations
`add_as`	additionally to a254 and a300, absorbance at certain wavelengths can be added to the table
`limits`	list with vectors containig upper and lower bounds of wavelengeth ranges to be fitted
`l_ref`	list with reference wavelengths, same length as limits
`S`	logical, include slope parameter in the table
`lref`	logical, include reference wavelength in the table
`p`	logical, include ps of the coefficients in the table
`model`	logical, include complete model in data frame
`Sint`	logical, wether the spectral curve is calculated interval-wise (`cdom_spectral_curve`)
`interval`	passed on to `cdom_spectral_curve`
`r2threshold`	passed on to `cdom_spectral_curve`
`cores`	number of cores to be used for parallel processing
`verbose`	logical, additional information is provided

The absorbance data is a data frame with the first column called "wavelength" containg the wavelength. Each other column contains the data from one sample. You can use absorbance_read to read in appropriate data.

The following spectral parameters are calculated:

$S_275-295$ slope between 275 and 295 nm calculated with nonlinear regression
$S_350-400$ slope between 350 and 400 nm calculated with nonlinear regression
$S_300-700$ slope between 275 and 295 nm calculated with nonlinear regression
SR slope ratio, calculated by $S_275-295$/$S_350-400$
E2:E3 ratio $a_250$/$a_365$
E4:E6 ratio $a_465$/$a_665$
$a_254$ absorbance at 254 nm
$a_300$ absorbance at 300 nm

Depending on available wavelength range, values might be NA. Additionally other wavelength limits can be defined. The slope ratio might fail in this case. For further details please refer to Helm et al. (2008).

A data frame containing the adsorption slopes and slope ratios in column, one line for each sample.

Helms, J., Kieber, D., Mopper, K. 2008. Absorption spectral slopes and slope ratios as indicators of molecular weight, source, and photobleaching of chromophoric dissolved organic matter. Limnol. Oceanogr., 53(3), 955–969 http://onlinelibrary.wiley.com/doi/10.4319/lo.2008.53.3.0955/pdf

data(absorbance)

a1 <- abs_parms(absorbance,cuvle=5, verbose = TRUE)
a2 <- abs_parms(absorbance,cuvle=5,l_ref=list(NA,NA,NA), lref=TRUE) # fit lref as well