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.
- Version0.2.3
- R version≥ 3.6.0
- LicenseMIT
- LicenseLICENSE
- Needs compilation?Yes
- cloneRate citation info
- Last release09/22/2023
Documentation
Team
Brian Johnson
Yubo Shuai
Show author detailsRolesAuthor, Copyright holderJason Schweinsberg
Kit Curtius
Insights
Last 30 days
This package has been downloaded 197 times in the last 30 days. Enough downloads to make a small wave in the niche community. The curiosity is spreading! The following heatmap shows the distribution of downloads per day. Yesterday, it was downloaded 6 times.
The following line graph shows the downloads per day. You can hover over the graph to see the exact number of downloads per day.
Last 365 days
This package has been downloaded 2,341 times in the last 365 days. Now we’re talking! This work is officially 'heard of in academic circles', just like those wild research papers on synthetic bananas. The day with the most downloads was Jul 23, 2024 with 25 downloads.
The following line graph shows the downloads per day. You can hover over the graph to see the exact number of downloads per day.
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Dependencies
- Imports5 packages
- Suggests8 packages
- Linking To6 packages