analyze_dominant: Estimate f and theta from dominant marker data

In kholsinger/Hickory: Analysis of within-population inbreeding and population differentiation

Description

Estimate f and theta from dominant marker data

Usage

analyze_dominant(
  genos,
  prior_pi = list(lower = 0.1, upper = 0.9),
  prior_f = list(lower = 0.01, upper = 0.2),
  prior_theta = list(lower = 0.01, upper = 0.2),
  f_zero = FALSE,
  f_one = FALSE,
  theta_zero = FALSE,
  theta_lp = FALSE,
  f_pop = FALSE,
  alpha_l = 0.1,
  alpha_p = 0.1,
  ...
)

Arguments

genos	A list in the format returned by read_marker_data()
prior_pi	A vector specifying lower and upper limits on pi
prior_f	A vector specifying lower and upper limits on f
prior_theta	A vector specifying lower and upper limits on theta
f_zero	TRUE for f = 0 model
f_one	TRUE for f = 1 model
theta_zero	TRUE for theta = 0 model
theta_lp	TRUE to estimate locus- and population-specific effects on theta
f_pop	TRUE to estimate population-specific f
alpha_l	"tightness" of prior on locus-specific differences in theta
alpha_p	"tightness" of prior on population-specific differences in theta
...	Optional arguments passed to rstan::sampling()

Value

An object of class stanfit returned by rstan::sampling()

kholsinger/Hickory documentation built on Jan. 9, 2022, 6:30 p.m.