NEWS
HMPTrees 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
HMPTrees 1.4 (2017-07-05)
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
HMPTrees 1.3 (2016-01-19)
CHANGES
- Added a function to compare paired data sets
HMPTrees 1.2 (2013-09-16)
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