Changes in version 1.3.3                        

NEW FEATURES

    o   updates in package vignette

BUG FIXES

    o   remove limitation of maximum typecode in the plot, now using rainbow()

                        Changes in version 1.3.2                        

BUG FIXES

    o   fix the returned posterior p

                        Changes in version 1.1.9                        

BUG FIXES

    o   NA bug when model fails

    o   using the length of the segment if shorter than maxk

                        Changes in version 1.1.8                        

NEW FEATURES

    o   add error catching in biomvRhsmm

    o   updates in package vignette

BUG FIXES

    o   fine tuning of memory usage for large count data structure

    o   minor bug fixes

                        Changes in version 1.1.7                        

NEW FEATURES

    o   add support of Rle like sparse data in mcols of large count data structure.

    o   add mclapply for parallel processing of different seqnames in biomvRhsmm

                        Changes in version 1.1.6                        

BUG FIXES

    o   fix nbinom emis estimateSegCommonDisp -> nbinomCLLDD

                        Changes in version 1.1.5                        

NEW FEATURES

    o   update biomvRGviz to have trackList returned when tofile=FALSE

BUG FIXES

    o   typo fix in function argument

                        Changes in version 1.1.4                        

NEW FEATURES

    o   update biomvRGviz to plot multiple samples in one, and more param

    o   plot method now defaults to multiple samples in one, sampleInOne=T

BUG FIXES

    o   fix states rank when prior.m=cluster 

                        Changes in version 1.1.3                        

NEW FEATURES

    o   the x slot in the returning object for biomvRhsmm now also contains the probability of associated state for each position

    o   the param slot in the returning object for biomvRhsmm now also contains the updated emission and sojourn parameters for each seqname and sample column

                        Changes in version 1.1.2                        

NEW FEATURES

    o   add a new clustering method for emission prior estimation

    o   add a new example section of DMR detection in the vignette

BUG FIXES

    o   switch off several data checking warnings, use normal cat() instead

                        Changes in version 1.1.1                        

NEW FEATURES

    o   add support of direct input of sojourn parameters as named list.

BUG FIXES

    o   suppress warnings generated when appending GRanges object for the output

                       Changes in version 0.99.3                        

NEW FEATURES

    o   add mvt and t to the emis.type and tmvtFit function

BUG FIXES

    o   fix shift index (-1) in pois and nbinom fitting	    

                       Changes in version 0.99.2                        

NEW FEATURES

    o   add log-Vertibi in c

    o   add normalizing factor for estimation of emis$p and soj$d

    o   add avgFunc to be used in average calculation, median and mean with trim, default to median

BUG FIXES

    o   fix shift index (-1) in pois and nbinom fitting	

                       Changes in version 0.99.1                        

NEW FEATURES

    o   in Bioc-devel