build_consensus_links: Build consensus links between cases (i.e. most often selected...

In mrajeev08/treerabid: Reconstruct Rabies Transmission Trees

Build consensus links between cases (i.e. most often selected progenitors for a given case)

Description

Build consensus links between cases (i.e. most often selected progenitors for a given case)

Usage

build_consensus_links(
  links_all,
  case_dates,
  lineages = NULL,
  known_progens = NULL,
  max_cycles = 100,
  link_all = FALSE
)

Arguments

links_all	output from build_all_links
case_dates	data.table with two columns id_case (id of case) and symptoms_started (date symptoms started of case without uncertainty)
lineages	a data table with two columns, id_case and lineage, designating a lineage assignment for each case, defaults to NULL which means trees wont be resolved to a phylogeny
known_progens	a numeric vector of case ids for which progenitors are known
max_cycles	how many cycles to look for (if lots of date uncertainty you may want to increase this but it will likely slow things down a lot!)
link_all	whether you want to try and force links between cases (that is even if a case is often identified as the beginning of a chain, you want to see if it can be assigned to another progenitor, i.e. when trying to link up all cases to a sampled set of lineages)

Value

a data.table with the case pairs most often linked in transmission tree and their probability (i.e. prop of times a given case was selected as a progenitor)

mrajeev08/treerabid documentation built on Oct. 15, 2024, 12:14 p.m.