staRdom (version 1.1.28)

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

Description

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

Usage

abs_parms(
  abs_data,
  cuvle = NULL,
  unit = c("absorbance", "absorption"),
  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
)

Value

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

Arguments

abs_data

data frame containing absorbance data.

cuvle

cuvette (path) length in cm, ignored if unit is absorption

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 indices 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

Details

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).

References

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 https://aslopubs.onlinelibrary.wiley.com/doi/10.4319/lo.2008.53.3.0955

Examples

# \donttest{
data(absorbance)

a1 <- abs_parms(absorbance, cuvle = 5, verbose = TRUE, cores = 2)
a2 <- abs_parms(absorbance, cuvle = 5,l_ref=list(NA,NA,NA), lref=TRUE, cores = 2) # fit lref as well
# }