run.process.Ap.batch: Process Particulate absorption spectra in batch mode

In belasi01/RspectroAbs: Processing absorbance spectra from spectrophotometer

Description

This high level function reads an ASCII file containing the list of samples to process. It calls process.Ap.

Usage

run.process.Ap.batch(log.file = "Ap_log_TEMPLATE.dat", data.path = "./")

Arguments

log.file	is the name of the ASCII file containing the list of samples to process (see details below).
data.path	is the path where the csv folder is located (txt folder in the case of ULTRAPATH). So the files must be stored in data.path/csv/. Default is "./".

Details

The most important thing to do before runing this programm is to prepare the log.file. This file contains 11 fields (TAB delimated) :

ID Unique ID of the sample

Repl A letter corresponding to the replicat (A,B,C,etc)

Station Station name

Date Date of sampling

Depth Depth of the sample

Vol Filtered volume in mL

Farea clearance area of particles on filter in m^2

blank.file ID if the reference blank filter

Ap.good Boolean quality control indicator (1=good ; 0 = not good)

NAp.good Boolean quality control indicator (1=good ; 0 = not good)

process Boolean (1=to be process ; 0 = to skip in the batch processing)

NAP.method String indicating the method is retained to derive phytoplankton absorption ("Measured", "Fitted", "BS90_1"", "BS90_2")

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