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. 2022 Dec 21;9(1):veac120. doi: 10.1093/ve/veac120

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© The Author(s) 2023. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 2. — Examples of twt simulation outputs for a model of cell dynamics in the latent reservoir. (top) Population dynamics simulated forward in time. Each line represents the population size of a different compartment. S = susceptible, I = infected. The dashed vertical line indicates the time of ART initiation. This plot was produced by calling the generic plot method on the S3 object from the twt function sim.outer.tree. (bottom) A tree simulated in reverse-time, relating 10 cells sampled from the latently infected compartment at τ = 0 and 30 from the actively infected compartment at $Inline graphic$ (Scenario 1), where $Inline graphic$ . Triangles represent transmission events, open circles represent transitions, and closed circles represent sampling times. Branches representing cell lineages in a latent state (Latentcomp_N) are collapsed prior to simulating virus evolution. This tree visualization was generated from the same S3 object using the R package ggfree (https://github.com/ArtPoon/ggfree).

Inline graphic — Examples of twt simulation outputs for a model of cell dynamics in the latent reservoir. (top) Population dynamics simulated forward in time. Each line represents the population size of a different compartment. S = susceptible, I = infected. The dashed vertical line indicates the time of ART initiation. This plot was produced by calling the generic plot method on the S3 object from the twt function sim.outer.tree. (bottom) A tree simulated in reverse-time, relating 10 cells sampled from the latently infected compartment at τ = 0 and 30 from the actively infected compartment at $Inline graphic$ (Scenario 1), where $Inline graphic$ . Triangles represent transmission events, open circles represent transitions, and closed circles represent sampling times. Branches representing cell lineages in a latent state (Latentcomp_N) are collapsed prior to simulating virus evolution. This tree visualization was generated from the same S3 object using the R package ggfree (https://github.com/ArtPoon/ggfree).