BSP | R Documentation |
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).
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
)
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
|
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 |
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 |
mu_unit |
The unit used for the mutation rate. Options are either "generation" or "time" |
save2disk |
Whether to save results to disk (default: TRUE) |
A list where the first element is a data.table with skyline data and the others are the BSPs.
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