ts_divergence: Calculate pairwise divergence between sets of individuals

In bodkan/spannr: A Simulation Framework for Spatiotemporal Population Genetics

Calculate pairwise divergence between sets of individuals

Description

Calculate pairwise divergence between sets of individuals

Usage

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 divergence value or a vector of divergence values (one for each window)

Examples

init_env()

# load an example model with an already simulated tree sequence
slendr_ts <- system.file("extdata/models/introgression_slim.trees", package = "slendr")
model <- read_model(path = system.file("extdata/models/introgression", package = "slendr"))

# load the tree-sequence object from disk
ts <- ts_read(slendr_ts, model) %>% ts_mutate(mutation_rate = 1e-8, random_seed = 42)

# 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) %>% .[order(.$divergence), ]

bodkan/spannr documentation built on Dec. 19, 2024, 11:43 p.m.