oXim (version 1.0.1)

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

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.

Details

fileMode must be a list contains filenames for Fish38, Fluid120 and Bluelike38. For directoryMode, it must be a list with a directory with Fish38, Fluid120 and Bluelike38 files in order to group and build final echograms.

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)