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    file, and outputs to an output file.

    The package contains a large selection of functions to manipulate CUI
    Co-occurrence matrices in the utils/datasetCreator/ directory. These are
    short scripts and generally require modifying the code at the top with
    user input paramaters specific for each run. These scripts include:

    applyMaxThreshold.pl -- applies a maximum co-occurrence threshold to the
    co-occurrence matrix

    applyMinThreshold.pl -- applies a minimum co-occurrence threshold to the
    co-occurrence matrix

    applySemanticFilter.pl -- applies a semantic type and/or group filter to
    the co-occurrence matrix.

    combineCooccurrenceMatrices.pl -- combines the co-occurrence counts of
    multiple co-occurrence matrices

    makeOrderNotMatter.pl -- makes the order of CUI co-occurrences not
    matter by updating the co-occurrence matrix file. (UMLS::Association
    generates co-occurrence files where order does matter, so the sentence
    'cui1 cui2' will only mark a co-occurrence between cui1 and cui2, but
    not between cui2 and cui1).

    removeCUIPair.pl -- removes all occurrences of the specified CUI pair
    from the co-occurrence matrix

    removeExplicit.pl -- removes any keys that occur in an explicit
    co-occurrence matrix from another co-occurrence matrix (typically the
    squared explicit co-occurrence matrix itself, which generates a
    prediction matrix, or the post cutoff matrix used in time slicing to
    generate a gold standard file)

    testMatrixEquality.pl -- checks to see if two co-occurrence matrix files
    contain the same data

    Also included are several subfolders with more specific purposes. Within
    the dataStats subfolder are scripts to collect various statistics about
    the co-occurrence matrices used in LBD. These scriptsinclude:

    getCUICooccurrences.pl -- a data statistics file that gets the number of
    co-occurrences, and number of unique co-occurrences for every CUI in the
    dataset

    getMatrixStats.pl -- determines the number of rows, columns, and entries
    of a co-occurrence matrix

    metaAnalysis.pl -- determines the number of rows, columns, vocabulary
    size, and total number of co-occurrences of a co-occurrence file, or set
    of co-occurrence files

    There is another folder containing scripts to square co-occurrence
    matrices. Squaring an explicit (A to B) co-occurrence matrix results in
    a co-occurrence matrix containing all implicit (A to C) connections.
    This is useful for time slicing and other analysis. Removal of the
    original explicit matrix is an additional step that is required if you
    wish to create a predictions matrix file for every CUI. This can be done
    with the removeExplicit.pl script. Squaring a co-occurrence matrix can
    be very computationally expensive, both in terms of ram and cpu. For
    this reason MATLAB scripts are preferred over perl scripts. Even using
    MATLAB ram can become an issue, and squaring sections of a matrix and
    combining them into a single output matrix may be necassary, but takes
    much longer. Scripts in the squaring folder include:

    convertForSquaring_MATLAB.pl -- functions to convert to and from ALBD
    and MATLAB sparse matrix formats

    squareMatrix.m -- MATLAB script to square a matrix while holding
    everything in ram. Faster, but requires more ram.

    squareMatrix_partial.m -- MATLAB script to square a matrix in chunks.
    Only loads parts of the matrix into ram at a time which makes squaring
    any size matrix possible, but potentially take impracticle amounts of
    time.

    squareMatrix_perl.pl -- squares a matrix in perl, but requires the most
    ram of any squaring method. The easiest method to use, but only
    practical for small datasets.

    The fromMySQL folder contains scripts that convery UMLS::Association
    databases to ALBD co-occurrence matrices. The files contained are:

    dbToTab.pl -- converts a UMLS::Association co-occurrence database to a
    sparse format co-occurrence matrix used for ALBD

    removeQuotes.pl -- removes quotes from lines in the co-occurrence matrix
    file after converting from a database (sometimes needed)

  REFERENCING
        If you write a paper that has used UMLS-Association in some way, we'd 
        certainly be grateful if you sent us a copy.

  CONTACT US
    If you have any trouble installing and using ALBD, please contact us
    directly if you prefer :

        Sam Henry: henryst at vcu.edu

        Bridget McInnes: btmcinnes at vcu.edu

  SOFTWARE COPYRIGHT AND LICENSE
        Copyright (C) 2017 Sam Henry & Bridget McInnes

        This suite of programs is free software; you can redistribute it and/or
        modify it under the terms of the GNU General Public License as published
        by the Free Software Foundation; either version 2 of the License, or (at
        your option) any later version.

        This program is distributed in the hope that it will be useful, but
        WITHOUT ANY WARRANTY; without even the implied warranty of
        MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
        Public License for more details.

        You should have received a copy of the GNU General Public License along
        with this program; if not, write to the Free Software Foundation, Inc.,
        59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.

        Note: The text of the GNU General Public License is provided in the file
        'GPL.txt' that you should have received with this distribution.