tgvaughan/MASTER

Issues

• Sample lineages from different populations

  #32 opened 11 years ago by sdwfrost
  6

• Multiple sampling of transmission tree

  #54 opened 2 years ago by ekankaka
  1

• populationName, reactionName, etc unnecessary

  #33 opened 2 years ago by tgvaughan
  1

• No post-simulation condition for non-inheritance simulations

  #34 opened 2 years ago by tgvaughan
  0

• JSON output mechanism wastes memory

  #30 opened 2 years ago by tgvaughan
  0

• Unit Tests

  #35 opened 2 years ago by tgvaughan
  2

• Clean up JSON output mechanism

  #18 opened 2 years ago by tgvaughan
  0

• Neater specification of moments.

  #17 opened 2 years ago by tgvaughan
  0

• frequency-dependent rates

  #25 opened 2 years ago by sdwfrost
  4

• master not in available in BEAST v2.7 packages

  #53 opened 2 years ago by ekankaka
  2

• Who infected whom

  #52 opened 2 years ago by thednainus
  1

• Possible typo in message

  #51 opened 3 years ago by aezarebski
  2

• BeastTreeFromMaster using taxonset instead of alignment input

  #50 opened 4 years ago by rbouckaert
  2

• Query about specifying conditionals in Predicate element

  #49 opened 5 years ago by jnarag
  2

• Trace history of particles?

  #45 opened 5 years ago by sdwfrost
  5

• iteration example?

  #46 opened 5 years ago by sdwfrost
  1

• Simple problem

  #48 opened 5 years ago by noahaus
  2

• Left/right ordering of child nodes not guaranteed in coalescent tree generation

  #19 opened 9 years ago by tgvaughan
  1

• Type changes at non-singleton nodes produce surprising output

  #42 opened 9 years ago by tgvaughan
  1

• Newick output hangs indefinitely for even moderately large graphs

  #43 opened 9 years ago by tgvaughan
  0

• No indication of simulations being finished

  #40 opened 9 years ago by tgvaughan
  0

• Problem with XML element in StructuredStochasticLogisticTreeSampled.xml

  #39 opened 10 years ago by maxbiostat
  1

• Setting nSamples doesn't give regular sampling

  #29 opened 10 years ago by tgvaughan
  1

• Finite time step trajectory probability calculations

  #37 opened 10 years ago by tgvaughan
  2

• URL invalid

  #38 opened 10 years ago by richelbilderbeek
  2

• duplicate reactions

  #24 opened 11 years ago by erikvolz
  2

• BeastTreeFromMaster messy and undocumented.

  #36 opened 11 years ago by tgvaughan
  1

• LineageSampler not found

  #31 opened 11 years ago by sdwfrost
  1

• Time-dependent rates

  #27 opened 11 years ago by tgvaughan
  1

• Big Refactor

  #26 opened 11 years ago by tgvaughan
  1

• Users reporting problems with recent versions of OS X

  #28 opened 11 years ago by tgvaughan
  5

• State of lineage at sampling

  #23 opened 11 years ago by erikvolz
  2

• NullPointerException during postProcessing, when simulationTime hit (no endCondition)

  #21 opened 12 years ago by denisekuehnert
  1

• NullPointerException in InheritanceTrajectory when simulationTime not specified

  #20 opened 12 years ago by denisekuehnert
  1

• LineageEndCondition exceeded

  #22 opened 12 years ago by denisekuehnert
  1

• Allow for ensembles of trees

  #15 opened 12 years ago by tgvaughan
  1

• Add support for BEAST tree generation

  #16 opened 12 years ago by tgvaughan
  1

• Implement string-based reaction specification

  #13 opened 12 years ago by tgvaughan
  1

• Update XML interface

  #12 opened 12 years ago by tgvaughan
  1

• Add reaction type annotation to graph nodes.

  #11 opened 12 years ago by tgvaughan
  1

• Add single-reaction wrapper for InheritanceReactionGroup

  #10 opened 12 years ago by tgvaughan
  1

• Allow timed start nodes.

  #7 opened 12 years ago by tgvaughan
  1

• Allow trajectories to have end conditions

  #6 opened 12 years ago by tgvaughan
  1

• Choose a better class name than InheritanceGraph

  #8 opened 12 years ago by tgvaughan
  1

• Fix rejection end conditions for inheritance graphs.

  #14 opened 12 years ago by tgvaughan
  1

• Find out why stochastic logistic inheritance model is failing.

  #9 opened 12 years ago by tgvaughan
  1

• Tree generation

  #3 opened 12 years ago by tgvaughan
  0

• JSON output for Trajectory and Ensemble objects.

  #5 opened 12 years ago by tgvaughan
  0

• Modularisation of output file generation

  #4 opened 12 years ago by tgvaughan
  0

• Model description in output JSON

  #2 opened 12 years ago by tgvaughan
  0