CHANGES IN HMPTrees VERSION 1.5

CHANGES

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

* Tidied up some code, comments and variable names

* Rewrote how trees are created

* Changed mergeDataSets to not calculate MLEs by default

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

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

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

* Simplified plotTreeDataMDS's arguments some



CHANGES IN HMPTrees VERSION 1.4

CHANGES

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

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

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


CHANGES IN HMPTrees VERSION 1.3

CHANGES

* Added a function to compare paired data sets



CHANGES IN HMPTrees VERSION 1.2

CHANGES

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

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

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

* Added more functionality/options to the plotTreeDataMDS function

* Changed the generateTree function 

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