In emvolz-phylodynamics/mlesky: Maximum likelihood estimation of effective population size through time, growth rates, and phylodynamic regressions

HIV example

We analyzed 399 HIV-1 sequences from Senegal between 1990 and 2014. All sequences are subtype CRF02_AG. treedater analysis shows a common ancestor around 1970 with LTT having rapid change in the early 1980s when the HIV epidemic was expanding.

Here is the mlesky analysis

require(mlesky)
treeHIV <- ape::read.tree( system.file('sn02ag2.0.nwk', package='mlesky') )
fit <- mlskygrid(treeHIV)
plot( fit, logy=FALSE)

Now we use cross-validation to find the smoothing parameter:

fit <- mlskygrid(treeHIV, tau = NULL, tau_lower = 0.1, tau_upper = 20 , ncpu = 6)
plot(fit, logy=FALSE) 

emvolz-phylodynamics/mlesky documentation built on Feb. 13, 2025, 1:47 p.m.