BSP: Generate Bayesian skyline plots
In carlopacioni/mtraceR: an R package to analyse migrate-n output

BSP	R Documentation

Generate Bayesian skyline plots

Description

BSP generates Bayesian skyline plots for each analysed locus (when relevant) and the sum over all loci. Plots are returned as ggplot objects and, when save2disk==TRUE, pdf files.

BSP will also return the data used to generate the BSPs as a data.table object and, when save2disk==TRUE, a csv file. These data are a 'clean up' version of these contained in the skyline file along with the upper and lower limits. The column "Time" is the rescaled "Age" (from migrate output) when gen and mu are provided. If you want to obtain the effective population size (recall that Migrate-n returns theta=xmuNe for population size, where x is the number of ploid - e.g. for mtDNA, 4 for nuclear loci, etc. - and mu is the mutation rate, if this is the parameter that you are considering) you could obtain this by calculating Ne=theta/(x * mu).

Usage

BSP(
  dir.in = NULL,
  skylinefile = NULL,
  dir.out = NULL,
  all.loci = TRUE,
  overall = TRUE,
  params = 1,
  gen = 1,
  mu = 1,
  mu_unit = "generation",
  save2disk = TRUE
)

Arguments

`dir.in`	The local folder containing skylinefile files (default: NULL)
`skylinefile`	The name of the skylinefile (default: NULL)
`dir.out`	The local path to store the results. If NULL (default) then `dir.out=dir.in`
`all.loci`	Whether the parameter should be plotted for each locus
`overall`	Whether the parameter should be plotted for the sum over all loci (when `nloci>1`)
`params`	A vector of parameter numbers to be plotted
`gen`	The generation time in unit of time (e.g. years)
`mu`	Mutation rate expressed either 'per generation' basis or in the same unit as `gen` (e.g. years)
`mu_unit`	The unit used for the mutation rate. Options are either "generation" or "time"
`save2disk`	Whether to save results to disk (default: TRUE)