inst/examples/ExfitMLE_bdK.R

In sophia-lambert/UDivEvo: A package for Unknown Diversity Diversification Analysis in Evolution

# Creating a phylogeny with 0.05 net diversification rate and 0.5 turnover rate.

set.seed(1234)
tree1 <- TESS::tess.sim.age(1, 100, lambda = 0.1, mu = 0.05, MRCA = TRUE, samplingProbability = 0.5)[[1]]
plot(tree1, root.edge = TRUE)

# Creating variables to give to arguments

tot_time <- max(TreeSim::getx(tree1))
Ntips <- ape::Ntip(tree1)
lamb_moments <- log(Ntips)/tot_time

# Fitting the birth-death k-sampling model

res_fitMCMC_M2 <- fitMLE_bdK(phylo = tree1,
                             tot_time = tot_time,
                             r = lamb_moments,
                             epsi = 0,
                             cond = "crown", YULE = FALSE,
                             dt = 0, rel.tol = 1e-10,
                             tuned_dichotomy = TRUE,
                             brk = 2000)

res_fitMLE_M2$parameters