bakR 0.4.0

• Added QC_check(), a function to perform quality control analysis with bakRFit objects. Looks for any problems in your data that will impair bakR’s performance, generates a number of diagnostic visualizations, and makes suggestions about what to do next.
• Fixed plot coloring bug in plotMA() and plotVolcano().
• Fixed bug that led to problems when the number of -s4U replicates > +s4U replicates in one or more Exp_IDs
• Implemented improved U-content adjustment for MCMC implementation. Also impacts accuracy of StanRateEst = TRUE mutation rate estimation strategy.
• Increased default number of features to use for StanRateEst mutation rate estimation strategy.
• Improved scaling of NSSHeat() output matrix columns.
• Created a new function NSSHeat2() that implements a different mechanism scoring function than NSSHeat().

bakR 0.3.0

• Optimized data preprocessing with data.table
• Increased simulation flexibility
• Added edge case error catching

bakR 0.2.5

• Added checks to bakRData validator
• Fixed bug in NSSHeatmap that prevented adjusting padj cutoff

bakR 0.2.4

• Addressed NOTEs to prepare for CRAN submission
• Removed previously deprecated function sim_bakRData()

bakR 0.2.3

• Expanded discussion of NSS analysis in vignette

bakR 0.2.2

• Fixed non-steady-state (NSS) uncertainty quantification
• Fixed uncertainty quantification for pulse-chase analysis
• Fixed fraction new estimation for pulse-chase analysis

bakR 0.2.1

• Added pulse-chase analysis option

bakR 0.2.0

• Improved default mutation rate estimation strategy
• Updated vignettes and added back non-steady state analysis strategy discussion
• Better commenting of fast_analysis (instead of opting for refactorization)

bakR 0.1.1

• Changed ordering of vignettes on website
• Got rid of unnecessary stan models and functions
• Fixed TL_stan output documentation
• Corrected missing namespace issues

bakR 0.1.0

• Made bakR public