process.Ap: Process raw optical depth to Ap spectra using filter-pad...

In belasi01/RspectroAbs: Processing absorbance spectra from spectrophotometer

Description

Spectrophotometer measures optical density (depth) (OD) or Absorbance (A), which are unit less. This program converts OD into absorption coefficent in per meter. Then a series of spectral analyses is performed.

Usage

process.Ap(
  sample,
  blank,
  Farea = NA,
  Vol.ml = NA,
  SpecType = NA,
  ID,
  Station,
  Repl,
  Depth,
  Date
)

Arguments

sample	is a data frame return by read.LAMBDA850 for the measured optical depth of the filter containing the particles. It contains two 2 columns for wavelength (wl) and Optical Depth (OD).
blank	is a data frame return by read.LAMBDA850 for the measured optical depth of a blank filter. It contains two 2 columns for wavelength (wl) and Optical Depth (OD).
Farea	is the filter clearance area of particles in m^2. This field is mandatory.
Vol.ml	is the volume filtered in ml. This field is mandatory.
SpecType	is a string indicating either "Ap" for the total particle or "Anap" for non-algal particles. This field is mandatory.
ID	is the sample ID.
Station	is the station code.
Repl	is a Capital Letter or number corresponding of the replicat ("A", "B",... or "1", etc)
Depth	is the depth of the sample in meters.
Date	is the date of sampling.

Value

Returns a list containing metadata provided to the function as well as the vector of OD corrected for blank, the OD of the blank filter and 3 estimation of particle absorption:

• Ap_Stramski folowwing Stramski et al, App. Optics 2015

• Ap_RG following Rottgers and Genhke, App. Opt. (2012)

• Ap_4.5 using a constant beta factor of 4.5 (see Rottgers and Genhke, 2012)

belasi01/RspectroAbs documentation built on July 27, 2020, 9:52 p.m.