2013-04-03  Maurice Berk <maurice@mauriceberk.com>

    * DESCRIPTION: Version is now 0.7

    * src/SME.c: fixed a missing guard around OpenMP code

2013-04-03  Maurice Berk <maurice@mauriceberk.com>

    * DESCRIPTION: Date is now 2013-04-03, Version is now 0.6

    * GPL-3, LICENCE: removed unnecessary files

    * man/*.Rd: updated author's email address, removed reference to LICENCE file

    * man/sme.Rd: removed an example to speed up the runtime

    * src/*.c: updated author's email address in comments

    * src/*.h: updated author's email address in comments

2013-04-02  Maurice Berk <maurice@mauriceberk.com>

    * DESCRIPTION: Date is now 2013-04-02, Version is now 0.5, author's email address updated

    * src/SME.c: OpenMP code is now properly guarded to ensure it's supported by the compiler

    * vignettes/Tutorial.Rnw: added a sentence explaining that OpenMP may not be supported depending
    on the platform

2012-09-18  Maurice Berk <maurice@mauriceberk.com>

    * DESCRIPTION: Date is now 2012-09-18

    * vignettes/Tutorial.Rnw: updated description of OpenMP functionality to reflect the default
    behaviour changing from using two threads to letting the OpenMP system automatically handle the
    number of threads. Fixed a broken reference to one of the plots

2012-09-04  Maurice Berk <maurice@mauriceberk.com>

    * DESCRIPTION: Date is now 2012-09-04

    * src/*.f: collated all individual LAPACK routines into a single file, LapackSubset.f

    * man/sme.list.Rd: updated documentation for sme.list to reflect the new default value for the
    parameter numberOfThreads

    * src/LinearAlgebra.c: changed to UNIX line endings

    * src/NelderMead.c: changed to UNIX line endings

    * src/NelderMead.h: changed to UNIX line endings

    * src/SME.h: changed to UNIX line endings

    * src/SME.c: changed to UNIX line endings

    * src/Makevars: changed to UNIX line endings

2012-09-01  Maurice Berk <maurice@mauriceberk.com>

    * Makevars: replaced PKG_FFLAGS=-frecursive with the more appropriate
    PKG_FFLAGS=$(SHLIB_OPENMP_FFLAGS)

2012-08-10  Maurice Berk <maurice@mauriceberk.com>

    * src/LinearAlgebra.c: removed any references to the LAPACK routines provided by R

    * Makevars: removed $(LAPACK_LIBS) from PKG_LIBS, added PKG_FFLAGS=-frecusrive to ensure local
    arrays in the new Fortran code are thread-safe

    * src/*.f: added those LAPACK 3.4.1 routines which are called from LinearAlgebra.c directly to
    the package, as the ones built-in to R are not thread-safe

    * src/SME.c: changed calls to nmmin() to NelderMead(), removed all omp critical pragmas

    * src/NelderMead.c, src/NelderMead.h: adapted the built-in R NelderMead search function nmmin()
    to be thread-safe

2012-08-07  Maurice Berk <maurice@mauriceberk.com>

    * src/SME.c: fixed a memory leak in calculateDegreesOfFreedom()

2012-07-31  Maurice Berk <maurice@mauriceberk.com>

    * R/sme.R: the default option for number of threads to use when carrying out multiple SME fits
    in parallel is now -1, which indicates OpenMP should manage the number of threads dynamically

    * src/SME.c: added the ability to let OpenMP manage the number of threads dynamically by
    passing a value of -1 for numberOfThreads to SMEOptimizationMultiple() and SMEMultiple()

2012-07-29  Maurice Berk <maurice@mauriceberk.com>

    * R/sme.R: removed superfluous names from degrees of freedom attribute returned by logLik.sme

2012-07-27  Maurice Berk <maurice@mauriceberk.com>

    * R/sme.R: fixed logLik.sme to read the degrees of freedom from the correct object field, fixed
    sme.list to properly return model residuals

2012-07-20  Maurice Berk <maurice@mauriceberk.com>

    * src/SME.c: removed original implementation of degrees of freedom calculation which had been
    commented out but remained in the file for some reason

2012-07-19  Maurice Berk <maurice@mauriceberk.com>

    * R/sme.R: added getRoughnessMatrix(), modified vcov.sme to accommodate this

    * man/getRoughnessMatrix.Rd: new help file to accompany the new function

    * NAMESPACE: updated namespace to export getRoughnessMatrix

2012-07-17  Maurice Berk <maurice@mauriceberk.com>

    * src/SME.c: minor optimizations to MStep()

2012-07-14  Maurice Berk <maurice@mauriceberk.com>

    * DESCRIPTION: Version is now 0.4

    * R/sme.R: sme.data.frame now correctly returns D as a matrix rather than a vector

    * src/SME.h: added N as a parameter to EStep()

    * src/SME.c: added N as a parameter to EStep(), minor optimizations to EStep(), improved
    debugging output when using the verbose parameter
