README.md

In leachth/ReadEKRaw_updated:

ReadEKRaw_updated

ReadEKRaw Description: parse the binary .raw files obtained from a Simrad Ex60 transceiver.

Input: file path name to a .raw file from a Simrad Ex60 transceiver

Output: list containing three lists: 
        (1) header  contains the header information for the file, and transceiver(s) including transceiver configuration and settings.
        (2) pings       contains data from each ping as a list 
        (3) GPS         GPS data for each ping in .raw file containing the following parameters:
                time            = time of ping in POSIXct format
                lat             = latitude in decimal degrees
                long            = longitude in decimal degrees
                fixquality      = fix quality of reading, 1 = fix, 0 = no fix
                numsatellites   = number of satellites tracking
                altitude        = measured as meters above sea level

Dependencies: ReadEKraw_Header ReadEKraw_DgHeader ConvertInttoUInt ReadEKraw_Configheader ReadEKraw_TransceiverConfig ReadEKraw_ReadSampledata ParseGPGGAstring

ReadEKRaw_ConvertPower Description: Converts power measurements obtained in the ReadEKRaw into Sv (dB re 1 m-1) is defined as the (Mean) Volume backscattering strength (MVBS) using the following formulas:

        Sv                  = power + TVG + (2*alpha*rangeCorrected) – CSv - Sac
        TVG                 = (20*log10 (rangeCorrected))
        CSv                 = 10 * log10 (pt* 10G/10) 2 * lambda2 * cv * tau * (10phi/10) / 32* pi2
        G                   = gain
        phi                 = equivalent beam angle
        cv                  = sound velocity; called c in the original Matlab code
        t                   = sample interval 
        alpha               = absorption coefficient    
        pt                  = transmit power
        tau                 = pulse length
        dR                  = cv * t / 2; calculate sample thickness (in range)
        lambda              = cv / f; calculate wavelength
        Sac                 = Sa correction
        rangecorrected      = power * dR

Input:  data structure from ReadEKRaw  (i.e. ReadEKRaw must be run first)

Output: data structure from ReadEKRaw with an additional vector of Sv and rangeCorrected (which is essentially depth) for each ping. This also add the gain and equivalent beam angel for the header to each ping element, this ensures that each ping element contains all of the information necessary to convert power to Sv.

FindBottom_updated Description: Finds the bottom depth for each ping in a ReadEKRaw_ConvertPower data object (i.e., you must run ReadEKRaw and then ConvertPower first). Adds a vector named bot.depth to each object in data$pings. Also generates an invisible vector called bottom.line where each element is the bottom depth at all indexed value in 1:length(data$pings), this vector is created for ease of plotting or other analyses.

Input: data structure from the ReadEKRaw_ConvertPower
    nf          = near field range in meters, user specified, defines the depth range from 0 - nf to exclude; defaults                 is 1 m
    d           = discrimination level in dB, pixels below this value are not considered when finding the bottom;                     default is -30 dB  
Output: 
data$ping$bot.depth     = data structure from ReadEKRaw_ConvertPower with an additional vector of bot.depth for each ping. 
data$bottom.line        = adds new list to data that is a vector that contains all of the bot.depth values for every ping in the file for ease of plotting

SubsetData_updated Description: function to subset data based on user specified start and end time or by GPS lat/longs; intended to subset data files into the individual transects from each lake that can then be plotted or further analyzed. Remember, that plotting function only works if the first ping in the data set is the start of the transect.

Input: data structure from ReadEKRaw_Convert Power as well as FindBottom2, although the FindBottom2 is not necessary.
    start   = time at start of transect or sampling period as character in format "YYYY-MM-DD HH:MM:SS GMT" or decimal degrees as a number with form c(lat, long)
    end     = same as above but for end time. 
    method  = specified by user as either "time" or "latlong", must match units in start and end

Output: A data object with all elements as input data but from start to end only.

CreateMatrix Description: creates data matrix for pings and depth intervals for sampling input, to be used for plotting or further data analysis. Echogram.pixel usesd CreateMatrix.

Input: 
    data                = data object from that comes out of ReadEKRaw(fname) & ReadEKRaw_ConvertPower(data). If matrix is to be constrained above the lake bottom then the data object must have also been processed by the FindBottom2(data). Currently handles data objects with 710 kHz frequency.
    nf                  = nearfield distance, offset below surface in meters to be excluded from matrix; default is 0 
    use.bottom.line     = Use the lake bottom as bottom depth of the matrix; default is FALSE
    bottom.line.offset  = value to specify depth offset in meters below (positive values) or above (negative values) the bottom line that are to be plotted; default is 0 m.
    threshold           = data with backscatter (dB) stronger than this value are turned to NA's  in data matrix. Use this to remove possible scatter from fish. Default is -30 dB.


Output: data matrix of backscatter for each ping at each depth interval.

Echogram.pixel Description: writes and echogram with key to a .png file

Input: data object from ReadEKRaw, ConvertPower and FindBottom
        filename            = file name in the form “filename.png”; must be specified so the file can be written
        height              = value in inches that specifies the height of the image; default is 5.
        width               = value in inches that specifies the width of the image; default is 7.
        ppi                 = resolution of image; default is 300, make smaller for smaller image files                   
        nlevels             = number of levels for color scale; default is 15
        plot.title          = character vector in quotes to label plot; default is “”
        key.title           = character vector in quotes of title of color key; default is “Sv"
        xlab                = character vector in quotes of title of color key; default is  “Index"
        nf                  = nearfield distance, offset below surface in meters to be excluded from plot; default is 1 
        use.bottom.line     = default is TRUE, when set to default only backscatter from the bottom line offset to the nf range are plotted. 
        bottom.line.offset  = value to specify depth offset in meters below (positive values) or above (negative values) the bottom line that are to be plotted; default is 1 m.
        threshold           = data with backscatter (dB) stronger than this value are excluded. Use this to remove possible scatter from fish; default is -30 dB.
        x                   = vector of values to be used for the x-axis. Must be the same length as number of pings; default is a vector 1:length(pings).
        zstart              = lowest value of z (backscatter); default is -70 dB
        zend                = highest value of z (backscatter); default is -30 dB
        y                   = vector of depth intervals form sample data; default is data$pings[[2]]$rangeCorrected. THIS SHOULD NOT BE CHANGED.
        ylim                = range of y values; default is rev(c(0, max(data$bottom.line + bottom.line.offset))), THIS SHOUKD NOT BE CHANGED.
        levels              = pretty separations for colors of z and scale bare. THIS SHOULD NOT BE CHANGED 
        xlim                = range of x values; default is range(x, finite=TRUE). THIS SHOULD NOT BE CHANGED.
        zlim                = range of z values base on zstart and zend, THIS SHOULD NOT BE CHANGED.

Output:  .png file of echogram with legend.

DistTransect Description: for each ping in data file estimates distance along transenct. Note that this is different as distance from shore. The start of the transect needs to be the first point in the data for this to work, so SubsetData must have already been used.

Input: data object from that comes out of ReadEKRaw(fname) & ReadEKRaw_ConvertPower(data) and SubsetData. The start of the transect needs to be the first point in the data for this to work, so SubsetData must have already been used.

Output: creates a new vector to data list named data$dist.alongtrans that contains distance from beginning of transect for each ping. Within each ping an element called GPS$dist.alongtrans is also created that indicated the distance along the transect for that specific ping.

leachth/ReadEKRaw_updated documentation built on May 23, 2019, 9:02 p.m.