Changes in version 1.5                         

CHANGES

    o   Changed the getMLEandLoglike function to return additional values and use weightCols instead of weight

    o   Tidied up some code, comments and variable names

    o   Rewrote how trees are created

    o   Changed mergeDataSets to not calculate MLEs by default

    o   Changed generateTrees arguments to allow for different number of reads per sample

    o   transformHMPTreetoHMP and transformHMPtoHMPTree are now internal functions since they don't really do much more than transposing data frames

    o   Stopped using 'samples' in several functions to select which trees to use.  Just pass in only the trees to use.

    o   Simplified plotTreeDataMDS's arguments some

                  Changes in version 1.4 (2017-07-05)                   

CHANGES

    o   Changed buildTree to not set anything greater than 1 to 1

    o   Added drop=FALSE to several functions to prevent single samples from crashing

    o   Made pi base::pi so it wouldn't have conflict

                  Changes in version 1.3 (2016-01-19)                   

CHANGES

    o   Added a function to compare paired data sets

                  Changes in version 1.2 (2013-09-16)                   

CHANGES

    o   Changed every function to expect the taxa to be listed as the rownames, rather than the first column

    o   Changed the parallel computing in the compareTwoDataSets functions to work on any OS and use the doParallel package

    o   Changed the plotTreeDataMDS and mergeDataSets functions to accommodate any number of data sets

    o   Added more functionality/options to the plotTreeDataMDS function

    o   Changed the generateTree function 

    o   Changed several functions to allow the use of splits besides a '.' in the taxa names