CHANGES: Log of significant changes between revisions

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# multic 0.4.3
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  - All p-values are no longer rounded including Wald score p-values.

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# multic 0.4.1
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  - p-values are no longer rounded. Previously, they were rounded to 4
    decimal places and reported as 0 if they were less than 0.0005.

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# multic 0.3.9
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  - Now suggests the package bdsmatrix so that gchol function can be
    accessed. (Previously in kinship package.)
  - Fixed bug in the generation of technical report.
  - Updated potentially unsafe calls to C++ fprintf function.
  - In order not be confused for S3 methods, functions plot.family.lods and
    t.rank have been renamed to tRank and plotFamilyLods respectively. The
    original names are still aliases, but they are not exported from the
    NAMESPACE.

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# multic 0.3.8
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  - Splus is no longer supported.

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# multic 0.3.7
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  - Support for NAMESPACE.
  - C++ code no longer writes to the console.
  - Splus no longer fully supported.
  - Because the plot.family.lods and t.rank functions were not S3 methods, 
    they have been deprecated and replaced with plotFamilyLods and 
    tRank respectively.

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# multic 0.3.5
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  - Now requires kinship2 package rather than archived kinship package.

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# multic 0.3.4
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  - Fixed multicString.h to match multicString.cpp - was causing problems
    for Solaris compilers.

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# multic 0.3.3
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  - Added merlin2mloci function.

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# multic 0.3.2
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  - To adhere to changes in R 2.6.0 regarding the return type of
    CHARACTER_VALUE function.  The return type is now 'const char*' rather
    than char*.

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# multic 0.3.1
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  - Updated licensing info in DESCRIPTION file and added LICENSE file to
    adhere to requests from CRAN.

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# multic 0.3.0
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  - sw2mloci function is now fully functional, although (in R) it
    cause memory mapping errors if the machine it's being run on has
    insufficient memory.

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# multic 0.2.2
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BUG FIXES
  - C++ declarations of long are replaced with 'Sint'.  Sint is defined
    as long for Splus and int for R.  This allows multic to run properly
    on systems where long and int are not the same size (such as most
    64-bit systems.

  - Major bug fix with regard to sorting mibd files and phi2 files.
    These were not being sorted properly on Linux systems due to differences
    in the behavior of 'sort' on Solaris and Linux.  It now works properly
    for both.

  - Fixed bug in calculating the size of a file.

  - The function sw2mloci requires a major bug fix.  Since this fix
    will require a great deal of time and effort, this function has
    been disabled in the current release.  It will be reincorporated
    in a future release.

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# multic 0.2
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NEW FEATURES
  - Added in the option to use the LRT instead of the Wald statistic
    when combining the various traits (addGE).

  - Allowed the user to specify the initial values (multic.control).

  - Added a plot to show all the lods scores of the top n most influential
    families to the max LOD score (plot.family.lods).

  - Improved the error message if share.out (or possibly, mloci.out)
    does not have the expected number of lines based on the famid
    argument.

BUG FIXES
  - Calculating the residuals and collapsing on the family was crashing
    with family of size one.

  - Allowed partial matching of arguments to the residuals.multic and
    fitted.multic methods.

  - Fixed the subset argument to multic.  It was not working when the
    subset was NOT a part of the data argument.

  - get.top.n.families would crash with multiple "global peak" values.

#############################################################################
# multic 0.1.1
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BUG FIXES
  - Converted CLK_TCK in the C++ code to CLOCKS_PER_SEC.  CLK_TCK is
    deprecated.

  - mkdir is only defined in Splus, not in R.  multic.mkdir was
    created to encapsulate this difference.

  - Removed the "multicInput" inconsistancy in examples/calls.q.
