Compute population specific FIS — pop

This function computes population specific FIS, using either the approach of Nei 1987 (as computed by hierfstat::basic.stats()) or of Weir and Goudet 2017 (as computed 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 estiamtes, 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