tgvaughan MASTER issues

tgvaughan / MASTER

A versatile simulation engine for stochastic population dynamics models.

http://tgvaughan.github.io/MASTER

GNU General Public License v3.0

22 stars 8 forks source link

issues

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Multiple sampling of transmission tree

#54 ekankaka closed 1 year ago
1
master not in available in BEAST v2.7 packages

#53 ekankaka closed 1 year ago
2
Who infected whom

#52 thednainus closed 1 year ago
1
Possible typo in message

#51 aezarebski closed 2 years ago
2
BeastTreeFromMaster using taxonset instead of alignment input

#50 rbouckaert closed 4 years ago
2
Query about specifying conditionals in Predicate element

#49 jnarag closed 5 years ago
2
Simple problem

#48 noahaus closed 5 years ago
2
Allow BeastTreeFromMaster to be re-initialised.

#47 christiaanjs closed 5 years ago
1
iteration example?

#46 sdwfrost closed 5 years ago
1
Trace history of particles?

#45 sdwfrost closed 5 years ago
5
Changed post-sim rejection count to any rejection.

#44 junniest closed 7 years ago
1
Newick output hangs indefinitely for even moderately large graphs

#43 tgvaughan closed 8 years ago
0
Type changes at non-singleton nodes produce surprising output

#42 tgvaughan closed 8 years ago
1
automatically set origin value for simulated BeastTreeFromMaster trees

#41 denisekuehnert closed 9 years ago
9
No indication of simulations being finished

#40 tgvaughan closed 9 years ago
0
Problem with XML element in StructuredStochasticLogisticTreeSampled.xml

#39 maxbiostat closed 9 years ago
1
URL invalid

#38 richelbilderbeek closed 9 years ago
2
Finite time step trajectory probability calculations

#37 tgvaughan closed 9 years ago
2
BeastTreeFromMaster messy and undocumented.

#36 tgvaughan closed 10 years ago
1
Unit Tests

#35 tgvaughan closed 1 year ago
2
No post-simulation condition for non-inheritance simulations

#34 tgvaughan closed 1 year ago
0
populationName, reactionName, etc unnecessary

#33 tgvaughan closed 1 year ago
1
Sample lineages from different populations

#32 sdwfrost closed 10 years ago
6
LineageSampler not found

#31 sdwfrost closed 10 years ago
1
JSON output mechanism wastes memory

#30 tgvaughan closed 1 year ago
0
Setting nSamples doesn't give regular sampling

#29 tgvaughan closed 9 years ago
1
Users reporting problems with recent versions of OS X

#28 tgvaughan closed 10 years ago
5
Time-dependent rates

#27 tgvaughan closed 10 years ago
1
Big Refactor

#26 tgvaughan closed 10 years ago
1
frequency-dependent rates

#25 sdwfrost closed 1 year ago
4
duplicate reactions

#24 erikvolz closed 10 years ago
2
State of lineage at sampling

#23 erikvolz closed 10 years ago
2
LineageEndCondition exceeded

#22 denisekuehnert closed 11 years ago
1
NullPointerException during postProcessing, when simulationTime hit (no endCondition)

#21 denisekuehnert closed 11 years ago
1
NullPointerException in InheritanceTrajectory when simulationTime not specified

#20 denisekuehnert closed 11 years ago
1
Left/right ordering of child nodes not guaranteed in coalescent tree generation

#19 tgvaughan closed 8 years ago
1
Clean up JSON output mechanism

#18 tgvaughan closed 1 year ago
0
Neater specification of moments.

#17 tgvaughan closed 1 year ago
0
Add support for BEAST tree generation

#16 tgvaughan closed 11 years ago
1
Allow for ensembles of trees

#15 tgvaughan closed 11 years ago
1
Fix rejection end conditions for inheritance graphs.

#14 tgvaughan closed 11 years ago
1
Implement string-based reaction specification

#13 tgvaughan closed 11 years ago
1
Update XML interface

#12 tgvaughan closed 11 years ago
1
Add reaction type annotation to graph nodes.

#11 tgvaughan closed 11 years ago
1
Add single-reaction wrapper for InheritanceReactionGroup

#10 tgvaughan closed 11 years ago
1
Find out why stochastic logistic inheritance model is failing.

#9 tgvaughan closed 11 years ago
1
Choose a better class name than InheritanceGraph

#8 tgvaughan closed 11 years ago
1
Allow timed start nodes.

#7 tgvaughan closed 11 years ago
1
Allow trajectories to have end conditions

#6 tgvaughan closed 11 years ago
1
JSON output for Trajectory and Ensemble objects.

#5 tgvaughan closed 11 years ago
0