Calculate the f2, f3, f4, and f4-ratio statistics

ts_f2(
  ts,
  A,
  B,
  mode = c("site", "branch", "node"),
  span_normalise = TRUE,
  windows = NULL
)

ts_f3(
  ts,
  A,
  B,
  C,
  mode = c("site", "branch", "node"),
  span_normalise = TRUE,
  windows = NULL
)

ts_f4(
  ts,
  W,
  X,
  Y,
  Z,
  mode = c("site", "branch", "node"),
  span_normalise = TRUE,
  windows = NULL
)

ts_f4ratio(
  ts,
  X,
  A,
  B,
  C,
  O,
  mode = c("site", "branch"),
  span_normalise = TRUE
)

Arguments

ts: Tree sequence object of the class slendr_ts
mode: The mode for the calculation ("sites" or "branch")
span_normalise: Divide the result by the span of the window? Default TRUE, see the tskit documentation for more detail.
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.
W, X, Y, Z, A, B, C, O: Character vectors of individual names (following the nomenclature of Patterson et al. 2021)

Value

Data frame with statistics calculated for given sets of individuals

Examples

if (FALSE)  # calculate f2 for two individuals in a previously loaded tree sequence
ts_f2(ts, A = "pop1_1", B = "pop2_1")

# calculate f2 for two sets of individuals
ts_f2(ts, A = c("pop1_1", "pop1_2", "pop1_3"),
          B = c("pop2_1", "pop2_2"))


if (FALSE)  # calculate f2 for two individuals in a previously loaded tree sequence
ts_f3(ts, A = "pop1_1", B = "pop2_1", C = "outgroup_1")

# calculate f2 for two sets of individuals
ts_f3(ts, A = c("pop1_1", "pop1_2", "pop1_3"),
          B = c("pop2_1", "pop2_2"),
          C = "outgroup_1")


if (FALSE)  # calculate f4 for single individuals
ts_f4(ts, W = "pop1_1", X = "pop2_1", Y = "pop3_1", Z = "pop4_1")

# calculate f4 for sets of individuals
ts_f4(ts, W = c("pop1_1", "pop1_2", "pop1_3"),
          X = c("pop2_1", "pop2_2"),
          Y = c("pop3_1", "pop3_2"),
          Z = c("pop4_1", "pop4_2"))


if (FALSE)  # calculate f2 for two samples in a previously loaded tree sequence
ts_f4ratio(ts, X = "test_1", A = "p1_1", B = "p2_1", B = "p3_1", C = "p4_1", O = "outgroup_1")