Estimate Growth Rates from Phylogenetic Trees
Growth rate estimate using MCMC
The 'cloneRate' package.
Generate tree from coalescence times
Check the inputs to growth rate functions
Growth rate estimate using the sum of internal lengths
Growth rate estimate using Maximum Likelihood
Growth rate estimate using the sum of shared mutations assuming a muta...
Simulate mutation-based birth and death branching trees
Simulate ultrametric birth and death branching trees
Get site frequency spectrum of a tree
Add poissonian mutations to an ultrametric tree(s)
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>.
Useful links