CircosHeatmap-aardio/dist/lib/r-library/Matrix/doc/SuiteSparse/CCOLAMD/README.txt

CCOLAMD: constrained column approximate minimum degree ordering
Copyright (C) 2005-2016.  Authors: Timothy A. Davis,
Sivasankaran Rajamanickam, and Stefan Larimore.  Closely based on COLAMD by
Davis, Stefan Larimore, in collaboration with Esmond Ng, and John Gilbert.
http://www.suitesparse.com
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SPDX-License-Identifier: BSD-3-clause

The CCOLAMD column approximate minimum degree ordering algorithm computes
a permutation vector P such that the LU factorization of A (:,P)
tends to be sparser than that of A.  The Cholesky factorization of
(A (:,P))'*(A (:,P)) will also tend to be sparser than that of A'*A.
CSYMAMD is a symmetric minimum degree ordering method based on CCOLAMD, also
available as a MATLAB-callable function.  It constructs a matrix M such
that M'*M has the same pattern as A, and then uses CCOLAMD to compute a column
ordering of M.

Requires SuiteSparse_config, in the ../SuiteSparse_config directory relative to
this directory.

To compile and install the ccolamd m-files and mexFunctions, just cd to
CCOLAMD/MATLAB and type ccolamd_install in the MATLAB command window.
A short demo will run.  Optionally, type ccolamd_test to run an extensive tests.
Type "make" in Unix in the CCOLAMD directory to compile the C-callable
library and to run a short demo.

CCOLAMD includes a simple top-level Makefile, which is optional.  All the work
is done via cmake.  Windows users can simply import the CMakeLists.txt into MS
Visual Studio.

"make" targets:

    make                compiles the CCOLAMD library;
                            "make install" will install in /usr/local/lib,
                            /usr/local/include, SuiteSparse/lib, and
                            SuiteSparse/include
    make demos          compiles and runs a few demos
    make library	compiles a C-callable library containing colamd
    make clean		removes all files not in the distribution,
                            but keeps the compiled libraries.
    make distclean	removes all files not in the distribution
    make local          compiles the CCOLAMD library;
                            "make install" will install only in
                            SuiteSparse/lib and SuiteSparse/include
    make install        installs the library
    make uninstall      uninstalls the library

See CCOLAMD/Doc/License.txt for the license.

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Related papers:

	T. A. Davis and W. W. Hager, Rajamanickam, Multiple-rank updates
	to a supernodal sparse Cholesky factorization, submitted.

	T. A. Davis, W. W. Hager, S. Rajamanickam, and Y. Chen, CHOLMOD: a
	sparse Cholesky update/downdate package, submitted.  CHOLMOD's
	nested dissection ordering relies on CCOLAMD and CSYMAMD to order
	the matrix after graph partitioning is used to find the ordering
	constraints.

	T. A. Davis, J. R. Gilbert, S. Larimore, E. Ng, An approximate column
	minimum degree ordering algorithm, ACM Transactions on Mathematical
	Software, vol. 30, no. 3., pp. 353-376, 2004.

	T. A. Davis, J. R. Gilbert, S. Larimore, E. Ng, Algorithm 836: COLAMD,
	an approximate column minimum degree ordering algorithm, ACM
	Transactions on Mathematical Software, vol. 30, no. 3., pp. 377-380,
	2004.

	"An approximate minimum degree column ordering algorithm",
	S. I. Larimore, MS Thesis, Dept. of Computer and Information
	Science and Engineering, University of Florida, Gainesville, FL,
	1998.  CISE Tech Report TR-98-016.

	Approximate Deficiency for Ordering the Columns of a Matrix,
	J. L. Kern, Senior Thesis, Dept. of Computer and Information
	Science and Engineering, University of Florida, Gainesville, FL,
	1999.

Authors:  Timothy A. Davis, Sivasankaran Rajamanickam, and Stefan Larimore.
	Closely based on COLAMD by Stefan I. Larimore and Timothy A. Davis,
        in collaboration with John Gilbert, Xerox PARC (now at UC Santa
        Barbara), and Esmong Ng, Lawrence Berkeley National Laboratory (much of
        this work he did while at Oak Ridge National Laboratory). 

CCOLAMD files:

    Demo	    simple demo
    Doc		    additional documentation (see ccolamd.c for more)
    Include	    include file
    Config          source for ccolamd.h
    Makefile	    optional Makefile
    CMakeLists.txt  for using cmake to build CCOLAMD
    MATLAB	    MATLAB functions
    README.txt	    this file
    Source	    C source code

    ./Demo:
    ccolamd_example.c	    simple example
    ccolamd_example.out	    output of colamd_example.c
    ccolamd_l_example.c	    simple example, long integers
    ccolamd_l_example.out   output of colamd_l_example.c

    ./Doc:
    ChangeLog	    change log
    License.txt     license

    ./Include:
    ccolamd.h	    include file

    ./MATLAB:
    ccolamd.m		MATLAB interface for ccolamd
    ccolamd_demo.m	simple demo
    ccolamd_install.m	compile and install ccolamd and csymamd
    ccolamd_make.m	compile colamd2 and symamd2
    ccolamdmex.c	MATLAB mexFunction for ccolamd
    ccolamd_test.m	extensive test
    ccolamdtestmex.c	test function for ccolamd
    Contents.m		contents of the MATLAB directory
    luflops.m		test code
    Makefile		Makefile for MATLAB functions
    csymamd.m		MATLAB interface for csymamd
    csymamdmex.c	MATLAB mexFunction for csymamd
    symamdtestmex.c	test function for csymamd

    ./Source:
    ccolamd.c		primary source code
    ccolamd_l.c		primary source code for int64_t version

    ./build:            where CCOLAMD is built
    .gitignore