combine_logs_and_traj: Combine BEAST log AND trajectory files after removing burnin

In emvolz-phylodynamics/sarscov2Rutils: Scripts to support preparation and analysis of SARS CoV 2 analyses

Description

Additionally, if some BEAST runs converged to a different tree space with different posterior, will exclude log files from runs with significantly lower posterior (analysis of variance) The 'Sample' column is modified and shared between the combined log and trajectory files so that they can be referenced against eachother

Usage

combine_logs_and_traj(
  logfns,
  trajfns,
  burnProportion = 0.5,
  ntraj = 200,
  ofn = NULL,
  ofntraj = NULL,
  pth = 0.01
)

Arguments

ntraj	This integer number of trajectories will be sampled from each trajectory file
ofn	If not NULL will save the combined log to this file name
ofntraj	If not NULL will save the combined traj to this file name
pth	Threshold p value for excluding logs based on sampled posterior values. If <0 will include all logs
bunrProportion	Will remove this proportion from the beginning of logs

Value

List with with combined logs and traj

emvolz-phylodynamics/sarscov2Rutils documentation built on Nov. 17, 2020, 9:22 a.m.