For a discussion on the difference between "site", "branch", and "node" options of the mode argument, please see the tskit documentation at https://tskit.dev/tskit/docs/stable/stats.html#sec-stats-mode.

ts_fst(
  ts,
  sample_sets,
  mode = c("site", "branch", "node"),
  windows = NULL,
  span_normalise = TRUE
)

ts_divergence(
  ts,
  sample_sets,
  mode = c("site", "branch", "node"),
  windows = NULL,
  span_normalise = TRUE
)

Arguments

ts

pyslim.SlimTreeSequence object

sample_sets

A list (optionally a named list) of character vectors with individual names (one vector per set)

mode

The mode for the calculation ("sites" or "branch")

windows

Coordinates of breakpoints between windows. The first coordinate (0) and the last coordinate (equal to ts$sequence_length) do not have to be specified as they are added automatically.

span_normalise

Divide the result by the span of the window? Default TRUE, see the tskit documentation for more detail.

Value

For each pairwise calculation, either a single Fst value or a vector of Fst values (one for each window)

For each pairwise calculation, either a single divergence value or a vector of divergence values (one for each window)