Release

Release of 07/2016: - Added AIC (Akaike Information Criterion) - Added modified BIC (user input) - Added possibility to use optimx instead of optim for the maximization step - Using compiler package to improve computing time - Improved code readability - Improved parallel computation handling4 - Solved conflicting name in simulation: cellularity of clone is now refered to as cellularit - Added option to keep all iteration models

-Perspectives: * tidy plot in cluster_plot * Reproducible test in R (QC only) * Reproducible testing in R+bash (QC+sciclone+pyClone) * Option to force single copy status - i.e. integrate QuantumCloneSingle in QuantumClone

Release of 10/12/2015: - Changed graph output to pdf - Fixed non-clustered graph name file

Release of 12/11/2015: - Added release tag on github - Checked for ggplot2 scheduled release

Release of 2/11/2015: - Correction of evolution plot - Adding content to vignettes - Added phylogenetic tree reconstruction and representation, along with examples - Added ImportFrom according to notes from R-devel: http://win-builder.r-project.org/

Release of 30/10/2015: * Major fix * - Post processing affected order of mutations but not of clustering. The clustering thus appeared erroneous in version 0.9.15 and 0.10.15

• Minor changes *
• Adding vignette release
• Changed dependency of doSNOW to doParallel
• Added data to decrease loading and check time
• Added function to plot results from output (by 2 elements)
• Added function to plot cellularity of clone in each sample (for time series, with proportion of mutation in each clone)