alchemical analysis features

alchemical-analysis announced in late 2017 that its features will be moved to alchemlyb. This is going to be a long and tedious process but it will have the following advantages

• tested (all code coming into alchemlyb is tested to > 90% coverage, with 95% as a goal)
• modular (functionality as library functions)
• Python 3 (and Python 2)

User input

The alchemlyb team welcomes user input: please raise an issue in the Issue Tracker for any alchemical-analysis features that you would really like to have in alchemlyb.

Please also feel free to edit this wiki page and contribute to the discussion.

Desired alchemical-analysis features

Please describe the feature and make a case for why you want it included. Add your name/GitHub handle; feel free to add yourself to any existing entries, too. Popular features are more likely to be migrated.

Overlap matrix

@orbeckst

• -w, --overlap Print out and plot the overlap matrix.
• unique functionality, quite useful in visual analysis of the data quality

More estimators

@orbeckst

• -m METHODS, --methods=METHODS
• missing estimators
  • TI_CUBIC #21
  • DEXP #22
  • IEXP #23
  • GINS #24
  • GDEL #25
  • UBAR #26
  • RBAR #27
  • BAR #28

Existing features

The following features already exist

• MBAR and TI estimators
• subsampling (with preprocessing.subsampling.statistical_inefficiency() (Does this correspond to the -n UNCORR, --uncorr=UNCORR feature??)
• discarding of initial time (-s EQUILTIME, --skiptime=EQUILTIME) and more flexible slicing with preprocessing.subsampling.slicing()
• Extract the energy data from the backward direction (-e, --backward) can be done with preprocessing.subsampling.slicing() (... I think ... check!)

Features in alchemlyb but not in alchemical-analysis

The following features only exist in alchemlyb

• equilibrium detection with preprocessing.subsampling.equilibrium_detection()