pop_fis: Compute population specific FIS

In tidypopgen: Tidy Population Genetics

Compute population specific FIS

Description

This function computes population specific FIS, using either the approach of Nei 1987 (with an algorithm equivalent to the one used by hierfstat::basic.stats()) or of Weir and Goudet 2017 (with an algorithm equivalent to the one used by hierfstat::fis.dosage()).

Usage

pop_fis(
  .x,
  method = c("Nei87", "WG17"),
  by_locus = FALSE,
  include_global = FALSE,
  allele_sharing_mat = NULL
)

Arguments

.x	a grouped gen_tibble (as obtained by using dplyr::group_by())
method	one of "Nei87" (based on Nei 1987, eqn 7.41) or "WG17" (for Weir and Goudet 2017) to compute FIS
by_locus	boolean, determining whether FIS should be returned by locus(TRUE), or as a single genome wide value (FALSE, the default). Note that this is only relevant for "Nei87", as "WG17" always returns a single value.
include_global	boolean determining whether, besides the population specific estimates, a global estimate should be appended. Note that this will return a vector of n populations plus 1 (the global value), or a matrix with n+1 columns if by_locus=TRUE.
allele_sharing_mat	optional and only relevant for "WG17", the matrix of Allele Sharing returned by pairwise_allele_sharing() with as_matrix=TRUE. As a number of statistics can be derived from the Allele Sharing matrix, it it sometimes more efficient to pre-compute this matrix.

Value

a vector of population specific fis (plus the global value if include_global=TRUE)

References

Nei M. (1987) Molecular Evolutionary Genetics. Columbia University Press Weir, BS and Goudet J (2017) A Unified Characterization of Population Structure and Relatedness. Genetics (2017) 206:2085

Examples

example_gt <- load_example_gt("grouped_gen_tbl")

# Compute FIS using Nei87
example_gt %>% pop_fis(method = "Nei87")

# Compute FIS using WG17
example_gt %>% pop_fis(method = "WG17")

# To include the global FIS, set include_global = TRUE
example_gt %>% pop_fis(method = "Nei87", include_global = TRUE)

# To return FIS by locus, set by_locus = TRUE
example_gt %>% pop_fis(method = "Nei87", by_locus = TRUE)

# To calculate from a pre-computed allele sharing matrix:
allele_sharing_mat <- pairwise_allele_sharing(example_gt, as_matrix = TRUE)
example_gt %>% pop_fis(
  method = "WG17",
  allele_sharing_mat = allele_sharing_mat
)

tidypopgen documentation built on Aug. 28, 2025, 1:08 a.m.