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Commits on Apr 17, 2026

• add superinfection unit tests

  WongDWai

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Commits on Apr 10, 2026

• working on inner tree tests

  WongDWai

  committed
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Commits on Mar 27, 2026

• wrote superinfection unit tests

  WongDWai

  committed
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Commits on Mar 10, 2026

• implemented #164

  ArtPoon

  committed
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Commits on Mar 6, 2026

• closes #161

  ArtPoon

  committed
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• working on #161, passing event and compartment info to phylo

  ArtPoon

  committed
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Commits on Mar 4, 2026

• Started to write unit test for InnerTree .relabel.inner.events

  ArtPoon

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Commits on Feb 26, 2026

• fixes #158, misspelled function name

  ArtPoon

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Commits on Feb 24, 2026

• writing unit tests for coalescence

  ArtPoon

  committed
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Commits on Feb 20, 2026

• working on .do.infection() for simInnerTree.R; I decided to separate coalescent rate from effective population size (pop.size), because the rate is in units of simulation time and not generations, …

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  ArtPoon

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Commits on Feb 19, 2026

• Added more unit tests for sim.inner.tree and InnerTree; added more accessor functionality to Pathogen class; renamed .do.transmission to .do.infection to avoid namespace collision between simInnerT…

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  ArtPoon

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Commits on Feb 18, 2026

• starting to write unit tests for InnerTree code

  ArtPoon

  committed
  8e2588f

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• updated Rd files

  ArtPoon

  committed
  1cb0d8f

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• reimplementing sim.inner.tree; creating new object class InnerTree

  ArtPoon

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Commits on Feb 17, 2026

• more unit tests

  ArtPoon

  committed
  a5ce116

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• fixed .reorder.events, postorder traversal was not outputting tip nodes

  ArtPoon

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Commits on Feb 13, 2026

• writing unit tests, some are broken

  ArtPoon

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• I think this fixes #156

  ArtPoon

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Commits on Feb 11, 2026

• trying a different approach to convert transmission history (outer events) into a tree

  ArtPoon

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Commits on Feb 10, 2026

• still debugging as.phylo.OuterTree, see 'as.phylo.OuterTree captures migration events' unit test in test_OuterTree.R; reopens #154

  ArtPoon

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• fixes #155; Host now tracks sampling compartment if it was sampled; HostSet provides access to this new variable; fixed checks for sampling numbers in sim.outer.tree

  ArtPoon

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• fixed #154, working on adding migration events to transmission tree now

  ArtPoon

  committed
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Commits on Feb 9, 2026

• working on #154

  ArtPoon

  committed
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• writing unit tests for as.phylo

  ArtPoon

  committed
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Commits on Feb 6, 2026

• wrote as.phylo.OuterTree function, trying to debug it now, see #153

  ArtPoon

  committed
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Commits on Feb 5, 2026

• fixed unit tests, host names are immutable now, sampling events are now recorded to the outer log - fixes #151

  ArtPoon

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• fixed some unit tests but #151 is still open

  ArtPoon

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Commits on Feb 4, 2026

• wrote unit tests for outer tree simulation (migration and transmission); added retired member variable to OuterTree class; added migration example YAML

  ArtPoon

  committed
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• renamed data frame for OuterTree

  ArtPoon

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• fixed unit tests

  ArtPoon

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Commits on Feb 3, 2026

• writing unit tests for sim.dynamics

  ArtPoon

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Commits on Feb 2, 2026

• writing unit tests for simDynamics

  ArtPoon

  committed
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• unit tests for OuterTree class

  ArtPoon

  committed
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• transmission rate matrix is now 3D, third dimesion corresponds to compartment of infecting Host, #150

  ArtPoon

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Commits on Feb 1, 2026

• fixing problems

  ArtPoon

  committed
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