PathoSurveilR v0.4.6

Bug fixes

• Fix bug in make_best_match_table when using numeric sample IDs

PathoSurveilR v0.4.5

Bug fixes

• Fixed both core and busco trees not being including in plot_tree

PathoSurveilR v0.4.4

Bug fixes

• Fixed invalid ggtree dependency error

PathoSurveilR v0.4.3

Bug fixes

• Fixed NA values for ANI in estimated_ani_match_table

PathoSurveilR v0.4.2

Improvements

• Replaced tree plotting functionality with heattree

PathoSurveilR v0.4.1

0.4.1

New features

• Added print_outdir_schema() function for displaying output directory schema information
• Added verbose and print_all options to print_outdir_schema()
• Added must_exist parameter to find_ps_data() function

Improvements

• Replaced the subset option with max_size and prefer_contextual parameters for better control
• Improved error messages in find_ps_paths() function
• Enhanced output metadata handling with name and description fallbacks

PathoSurveilR v0.4.0

Rewrite of how paths are found and files are parsed in order to make a single generic functions rather than one for each output.

PathoSurveilR v0.3.1

• fix bug in make_best_match_table when all matches are NA

PathoSurveilR v0.3.0

Changes

• Renamed package to PathoSurveilR since there is already a psminer on CRAN.
• Lots of small bug fixes
• Better heatmap printing
• Nearly all functions have examples that run now

psminer v0.2.0

First release with consistent API, but still likely contains errors and unimplemented features.