FAVITES-Lite v1.0.3

• Accidentally forgot to delete a debugging line in the "Truncated Normal" mutation rates model in the previous release

FAVITES-Lite v1.0.2

• Fixed bug in "Truncated Normal" mutation rates model
  • FAVITES-Lite is using the notation where a is the minimum and b is the maximum of the truncated distribution
    • In other words, the truncated distribution is in the range [a, b]
  • However, SciPy defines a and b as "standard deviations away from loc"
  • I added a helper function that takes a and b in the "min" and "max" notation, converts them, and then calls the SciPy function
  • The "Truncated Normal" sample times model was actually correct before (I was doing the conversion between notations here, just not in the mutation rates model), but I've updated it to use this new helper function
  • The "Truncated Exponential" sample times model was unaffected by this bug and has remained as-is

FAVITES-Lite v1.0.1

• Add support for symlink to favites_lite.py
  • Previously, favites_lite.py would not be able to find global.json if you create a symlink to run the script
  • Common use case: install the FAVITES-Lite folder in some global directory (e.g. /usr/local/bin/FAVITES-Lite) and make a symlink in your PATH (e.g. /usr/local/bin/favite_lite.py points to /usr/local/bin/FAVITES-Lite/favites_lite.py)

FAVITES-Lite v1.0.0

• Added the ability to provide a RNG seed

FAVITES-Lite v0.0.5

• Added support for epidemics with just 1 introduction
  • For "Viral Phylogeny (Seeds)", select "Single Introduction"

FAVITES-Lite v0.0.4

• Added Config Designer web app: https://niema.net/FAVITES-Lite

FAVITES-Lite v0.0.3

• Added more descriptive import and missing dependency errors
• Refactored how GEMF plugins infer infectious states
  • While doing this, I fixed a bug in the SEIR model implementation (S->E transitions weren't being counted as "infection events")

FAVITES-Lite v0.0.2

• Changed GEMF to move output files instead of copying
  • Saves time and space for big runs
• Added helper script to plot transmission states over time
• Added SAPHIRE and SAAPPHIIRE models

FAVITES-Lite v0.0.1

• Initial release