Tracer_Addon: Tracer Addon Function

In OJWatson/evoflution: Forward in time epidemic and genetic simulator with a focus on flu

Description

This function links with Tracer_Accumulation by creating the summary.txt file needed, by loading the log files as needed and first writing it.

Usage

  Tracer_Addon(cmd = paste("\"C:\\Users\\Oliver\\GoogleDrive\\AcademicWork\\Imperial\\O15-12\\BEAST\\BEAST v1.8.2\\bin\\loganalyser.cmd\""),
  file.dir, log.dir, reps, replicate.name = "replicate")

Arguments

cmd	shellscript path name for loganalyser.cmd. Tracer Addon uses the internal function system(), so path must be written accordingly.
file.dir	directory where the sumamry.txt file will be written to
log.dir	directory from which the log files are to be read from
reps	number of reps within the log.dir

Details

Tree Statistics pulled are internally coded to be the posterior, clock rate, growthRate, ePop and TMRCA.

The summary statistics pulled are internally coded to be the mean, standard error, median, HPD 95

The output is written to file for further use

Value

writes summary.txt file

OJWatson/evoflution documentation built on May 7, 2019, 8:32 p.m.