Reading biological data

The initial processing of biological data is done by the program implemenBiologicalData, which uses the routine readSamples in the notebook STUVdata

The routine implementBiologicalData reads and concatenates all files of biological data specified in teh variable biologicalFiles. It reports whether samples are common to several files and the series numbers read. The reporting is done on the notebook projectNotebook, which must have been generated beforehand. The concatenated file is processed by the routine readSamples in the notebook STUVdata and gives the output as the lists individInformation for data on V-lines and sampleInformation for data on U-lines. In addition the list timeSamples is generated, containing the time in number of days since the beginning of startMonth for each sample, assuming for simplicity that there are 30 days in each month. The routine readSamples reads the file stuvfile where a file of STUV data has been stored as a Mathematica list of strings, one record for each STUV-line.

    Global inputs

        stuvfile
        dataOrigin    STUV or AB
        usespecies
        lowlat
        highlat
        lowlon
        highlon

    Outputs

        individInformation
        sampleInformation
        points
        nations    Strings
        vesselcodes
        gears
        distances
        qualities
        openings
        doorspreads
        stationtypes
        maxdepths
        ships
        quadrants
        dates
        depths
        series
        catchweights
            Seriesnumber
            Species    String
            Catch weight (kg)
            Catch number

The following filters are implemented

    gearFilter    List of 4-digit integers
    qualityFilter    List of integers The Mathematica list individInformation holds individ information from IMR biological samples. Each entry has the format:

    Series number
    Species            String
    List of
        Length
        Weight
        Age
        Sex
        Maturity stage
        Special maturity stage
        First growth zone
        Last growth zone
        Readability
    Multspec area
    Part number

Time information for each station are hold in the list dates, with entries {year,day,month,hour}

Station numbers are held in the list series with entries {series number,station number}. The series number must be used to couple individs to stations

Positions are held in the list points with entries {{latdeg,latmin},{londeg,lonmin}} The Mathematica list sampleInformation holds the length distribution (U-line) of the sample. Each entry has the format:

Sample number
Species
Length distribution, list of
    Interval
    Lower length
    List of numbers
    Weight of sample (kg)
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