get_elapsed_time_tree: Gets elapsed time tree with optional mutational aquisition...

In NickWilliamsSanger/rsimpop: Simulates Cellular Evolution using a Continous Time Birth Death Model

Gets elapsed time tree with optional mutational aquisition modelling. Uses the model burden ~ sum(pois(mutatrateperdiv))+pois(backgroundrate*duration) If mutrateperdivision is not provide the function returns the ultrametric elapsed time tree. Note: the tree that comes out of sim_pop has branch lengths=number of symmetric divisions (i.e. edge_length=ndivs)

Description

Gets elapsed time tree with optional mutational aquisition modelling. Uses the model burden ~ sum(pois(mutatrateperdiv))+pois(backgroundrate*duration) If mutrateperdivision is not provide the function returns the ultrametric elapsed time tree. Note: the tree that comes out of sim_pop has branch lengths=number of symmetric divisions (i.e. edge_length=ndivs)

Usage

get_elapsed_time_tree(
  tree,
  mutrateperdivision = NULL,
  backgroundrate = NULL,
  odf = 1
)

Arguments

tree	simpop phylo. output from sim_pop or get_subsampled_tree.
mutrateperdivision	numeric. Mutation rate per division
backgroundrate	numeric. Negative Binomial or Poisson Distributed Mutation count
odf	numeric. Overdispersion factor.

Value

simpop/phylo - with branch lengths defined as above (sometimes stochastic)

NickWilliamsSanger/rsimpop documentation built on Sept. 6, 2024, 12:42 a.m.