LineageHomology_w_uncertainty: LineageHomology_w_uncertainty

In magnusnosnes/LineageHomology: Transmission Lineages From Maximum Likelihood Mappings

LineageHomology_w_uncertainty

Description

LineageHomology_w_uncertainty returns the same outputs as LineageHomology. LineageHomology counts transmission lineages according to state transitions between ancestral and descendant nodes that have a probability higher than 50 percent. LineageHomolog_w_uncertainty instead samples states from the posterior probability of states for each node. Thus, the transmission lineage division is probabilistic and retains the uncertainty in the posterior distribution if one runs multiple times, e.g., using base::replicate() (see examples).

Usage

LineageHomology_w_uncertainty(
  tree,
  ace_nodes,
  ace_tips,
  give_tips = NA,
  start_time = NA
)

Arguments

tree	Phylogenetic tree
ace_nodes	Node probabilities in ace format
ace_tips	Tip probabilities in ace format
give_tips	Constrain the computations to a set of tips, e.g. all the names of the tips in a certain state (e.g. one specific geographical location).
start_time	Date of root in the phylogeny.

Value

See LineageHomology for descriptions of the returns.

Examples

## Not run: 
multi_counts = pbreplicate(
  100,
  LineageHomology::LineageHomology_w_uncertainty(
    tree,
    ace_nodes = test$lik.anc,
    give_tips = Norwegian_tips,
    ace_tips = to.matrix(Locations, seq = c("Norway", "RoW")),
    start_time = start_date
  )
)

## End(Not run)

magnusnosnes/LineageHomology documentation built on April 17, 2025, 6:30 p.m.