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cloneRate: Estimate Growth Rates from Phylogenetic Trees
Quickly estimate the net growth rate of a population or clone whose growth can be approximated by a birth-death branching process. Input should be phylogenetic tree(s) of clone(s) with edge lengths corresponding to either time or mutations. Based on coalescent results in Johnson et al. (2023) <doi:10.1093/bioinformatics/btad561>. Simulation techniques as well as growth rate methods build on prior work from Lambert A. (2018) <doi:10.1016/j.tpb.2018.04.005> and Stadler T. (2009) <doi:10.1016/j.jtbi.2009.07.018>.
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Package details |
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| Author | Brian Johnson [cre, aut, cph] (<https://orcid.org/0000-0002-9477-4677>), Yubo Shuai [aut, cph], Jason Schweinsberg [aut, cph] (<https://orcid.org/0000-0002-4152-0059>), Kit Curtius [aut, cph] (<https://orcid.org/0000-0002-2678-0960>) |
| Maintainer | Brian Johnson <brian.d.johnson97@gmail.com> |
| License | MIT + file LICENSE |
| Version | 0.2.3 |
| URL | https://github.com/bdj34/cloneRate https://bdj34.github.io/cloneRate/ |
| Package repository | View on CRAN |
| Installation |
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