readEchograms: Takes outputs from Echopen and generates a matrix to...

In oXim: Oxycline Index from Matrix Echograms

Description

This function search outputs of Echoopen for Fluid-like, Blue noise and Fish and use them to make a filtered matrix to calculate the Oxycline limits.

Usage

readEchograms(fileMode = NULL, directoryMode = NULL, validFish38 = c(-100,
  -21), validBlue38 = c(-100, -56), upLimitFluid120 = -53,
  pinInterval = 50, date.format = "%d-%m-%Y %H:%M:%S", ...)

Arguments

fileMode	List with needed variables to read single Matlab files. See details below.
directoryMode	List with needed variables to read Matlab files from directory. See details below.
validFish38	Range of valid values for Fish-38kHz.
validBlue38	Range of valid values for Blue-38kHz.
upLimitFluid120	Upper limit for Fluidlike-120kHz.
pinInterval	Time threshold (in secs) to consider separate two matrices (echograms).
date.format	A character string. The default method is %Y-%m-%d %H:%M:%S.
...	Extra arguments (not used for now).

Details

fileMode must be a list with the next structure: fish38_file (directory for fish38 file), blue38_file (directory for blue38 file) and fluid120_file (directory for fluid120 file).

Similarly, directoryMode must be a list with the next structure: directory (folder where the files are storaged), fish38_pattern (text pattern for recognizing fish38 files), blue38_pattern (text pattern for recognizing blue38 files) and fluid120_pattern (text pattern for recognizing fluid120 files).

Examples

fileMode <- list(fish38_file   = system.file("extdata", "fish38.mat", package = "oXim"),
                 fluid120_file = system.file("extdata", "fluid120.mat", package = "oXim"),
                 blue38_file   = system.file("extdata", "blue38.mat", package = "oXim"))
echoData <- readEchograms(fileMode = fileMode)
print(echoData)

oXim documentation built on May 1, 2019, 8:20 p.m.