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Commits on Jun 16, 2026

• Merge pull request #174 from PoonLab/dev

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• closes #170

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• wrote unit tests to troubleshoot #173, worked on #170

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Commits on Jun 1, 2026

• potential fix for #172

  ArtPoon

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• allow user to reposiiton legend for plot.OuterTree

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Commits on May 26, 2026

• Merge branch 'dev' of https://github.com/PoonLab/twt

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Commits on May 12, 2026

• make time available, #170

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Commits on Apr 17, 2026

• Merge pull request #172 from PoonLab/test-superinf

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• Update simInnerTree.R

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• add superinfection unit tests

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Commits on Apr 10, 2026

• working on inner tree tests

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Commits on Apr 8, 2026

• Add SI visualization and fix .do.infection NULL crash for untracked recipients

  WongDWai

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Commits on Mar 27, 2026

• wrote superinfection unit tests

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Commits on Mar 15, 2026

• updated README, added first vignettes Rmd

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Commits on Mar 13, 2026

• Merge pull request #169 from PoonLab/dev

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• updated README

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Commits on Mar 12, 2026

• updating README

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• added print function for Pathogen, closes #165; updated time when coalescing Pathogen lineages in root Host, fixes #166

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• print generics for Host and HostSet, #165

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Commits on Mar 10, 2026

• print generics for Dynamics, OuterTree, InnerTree, #165

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• implemented #164

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Commits on Mar 6, 2026

• progress on #164

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• starting to work on #164 at the same time as #163"

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• starting to implement contemporaneous sampling #160

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• closes #161

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

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Commits on Mar 5, 2026

• fixed time discordance but compartment is still not being labelled correctly, see #161

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• partial implementation of #161

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• fixes #163

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Commits on Mar 4, 2026

• fixes #162

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

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• updated Rd files"

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Commits on Mar 2, 2026

• finished writing code for as.phylo.InnerTree

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• work in progress, as.phylo.InnerTree'

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Commits on Feb 27, 2026

• working in as.phylo.InnerTree, wrote relabelling function

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