Calculate diversity in given sets of individuals
ts_diversity(
ts,
sample_sets,
mode = c("site", "branch", "node"),
windows = NULL,
span_normalise = TRUE
)
Tree sequence object of the class slendr_ts
A list (optionally a named list) of character vectors with
individual names (one vector per set). If a simple vector is provided, it
will be interpreted as as.list(sample_sets)
, meaning that a given
statistic will be calculated for each individual separately.
The mode for the calculation ("sites" or "branch")
Coordinates of breakpoints between windows. The first
coordinate (0) and the last coordinate (equal to ts$sequence_length
)
are added automatically)
Divide the result by the span of the window? Default TRUE, see the tskit documentation for more detail.
For each set of individuals either a single diversity value or a vector of diversity values (one for each window)
if (FALSE) #' # collect sampled individuals from all populations in a list
sample_sets <- ts_samples(ts) %>%
split(., .$pop) %>%
lapply(function(pop) pop$name)
# compute diversity in each population based on sample sets extracted
# in the previous step
ts_diversity(ts, sample_sets) %>% dplyr::arrange(diversity)