phybreak 0.2.0

Major changes

• Datasets added
• Vignette phybreak_intro added
• Use more samples per host, with changes in data input, the phybreak object structure, and plotting
• Added mcmc-update steps for only the within-host phylogenetic minitree topology (not used by default)
• Added transmission tree plotting function plotTrans
• Data entry through new S3-class phybreakdata
• Simulation with sim.phybreak results in phybreakdata-object, that can directly be plotted
• MCMC progress shown on screen (10 sec intervals)

Minor changes

• Faster simulation and phybreak construction with long sequences.
• Automatic calculation of initial value for mu
• Reference date in phybreak object (d-slot) referring to t = 0, used for transtree and plot
• Minor changes in get.phybreak functions

BUG FIXES

• Fixed bug in transtree with Edmonds method (index case could have been incorrect)
• Correct on-screen log-likelihood during MCMC
• Bug in sim.phybreak giving error with option output.class = “obkData”

phybreak 0.1.1

BUG FIXES

• Solves issue with irreconcilable MCC trees in phylo-class vs table-form (#1) (reported by Mark Schultz)
  
• Solves errors with OS X 10.9 Mavericks