IOPs.go: IOPs data processing launcher

In belasi01/Riops: IOPs data processing

IOPs data processing launcher

Description

This function launches the IOPs data processing, which constists in applying various corrections and calibration to measured inherent optical properties (IOPs) of seawater constituents using various commercial instruments (see Details).

Usage

IOPs.go(report = FALSE, output.aTOT.COPS = FALSE, cast = "down",
  depth.interval = c(0.75, 2.1), a.instrument = "ASPH")

Arguments

report	is a logical parameter indicating whether or not a PDF report is produced using knitr. Default is FALSE.
output.aTOT.COPS	is a logical parameter indicating whether or not the spectral absorption is needed for COPS processing. IMPORTANT: a COPS folder with files preliminarly processed using the Cops package must be present in the folder YYYYMMDD_StationXXX (see Details). The Cops processing creates a file named absorption.cops.dat that will be automatically edited if output.aTOT.COPS=TRUE. The default is FALSE.
cast	If output.aTOT.COPS=TRUE, cast will indicate whether the down cast or the up cast will be used to average the non-water absorption. The default is "down"
depth.interval	If output.aTOT.COPS=TRUE, this parameter will indicates the depth interval for which the non-water absorption will be avaraged. The default is c(0.75,2.1)
a.instrument	If output.aTOT.COPS=TRUE, this parameter will indicate whether the non-water absorption will be taken from the a-sphere (ASPH) or the ac-s (ACS). The default is ASPH.

Details

IOPs.go processes data files found in each directories specify in the file named directories.for.IOPs.dat. NOTE: it is important to create one folder per cast following this convention:

• ../YYYYMMDD_StationXXX/PACKAGENAME/

where XXX is the station ID (with out "_" because it creates problems with the LaTex report) and PACKAGENAME is the name of the package. It could be anything.

For each directory specifyed in directories.for.IOPs.dat, four ASCII files will be necessary in addtion to the files coming from the instruments located in the directory. The ASCII files are:

• cast.info.dat: This file contains information relative to the current IOP profile;

• cal.info.dat: This file contains information relative to the instrument calibration;

• instruments.dat: This is a list of instruments currently supported by Riops. User should put 1 when the instrument present on the optical package. The instruments supported are the following (as on June 1st 2016):

  • HS6: A Hydroscat-6 from Hobilabs

  • ASPH: An a-sphere from Hobilabs

  • FLECO: An ECO triplet from Wet Labs. This was costumized for CDOM fluoresece with ex 379 and emission 420, 460 and 500nm

  • CTD.UQAR: A SBE19+ CTD from Seabird

  • CTD.DH4: A microCAT CTD from SeaBird

  • ACs: An AC-s from Wet Labs

  • BB9: A BB9 from Wet Labs

  • BB3: A BB3 from Wet Labs

  • FLBBCD: An ECO triplet from Wet Labs with chlorophyll fluorescence, bacskattering and CDOM fluorescence

  • FLCHL: A chlorophyll fluorescence meter from Wet Labs

  • LISST: A LISST from Sequoia;

• DH4.ports.dat: This file indicate on which port each instrument were attach to the DH4. It is therfore not necessary if the package does not include a DH4 to log the data

If IOPs.go is run without these files, they will be created automatically by the program and the user will be prompted to edit them.

Please read correct.merge.IOP.profile for a detailed description of the content of cast.info.dat, cal.info.dat and DH4.ports.dat.

Author(s)

Simon Belanger

See Also

correct.merge.IOP.profile, process.IOPs

belasi01/Riops documentation built on Sept. 5, 2022, 6:38 p.m.