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

Tree sequence object of the class slendr_ts

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)

Examples

if (FALSE)  # compute F_st between two sets of individuals in a given tree sequence ts
ts_fst(ts, sample_sets = list(afr = c("AFR_1", "AFR_2", "AFR_3"),
                              eur = c("EUR_1", "EUR_2")))


if (FALSE)  #' # collect sampled individuals from all populations in a list
sample_sets <- ts_samples(ts) %>%
  split(., .$pop) %>%
  lapply(function(pop) pop$name)

# compute the divergence between individuals from each sample set (list of
# individual names generated in the previous step)
ts_divergence(ts, sample_sets) %>% dplyr::arrange(divergence)