Documentation

msmtools provides these packages to perform estimation and further analysis of Markov models.

• estimation - MSM estimation from data (msmtools.estimation)
  • Countmatrix
  • Connectivity
  • Estimation
  • Sampling
  • Bootstrap
  • Priors
• analysis - MSM analysis functions (msmtools.analysis)
  • Validation
  • Decomposition
  • Expected counts
  • Passage times
  • Committors and PCCA
  • Fingerprints
  • Sensitivity analysis
• flux - Reactive flux an transition pathways (msmtools.flux)
  • TPT-object
  • Reactive flux
  • Reaction rates and fluxes
  • Pathway decomposition
• dtraj - Discrete trajectories functions (msmtools.dtraj)
  • Discrete trajectory io
  • Simple statistics
  • Sampling trajectory indexes
• generation - MSM generation tools (msmtools.generation)
  • Metropolis-Hastings chain