doBoot: Function to run a bootstrap iteration

In statdivlab/happi: a hierarchical approach to pangenomics inference

Function to run a bootstrap iteration

Description

Function to run a bootstrap iteration

Usage

doBoot(
  happi_results_boot,
  h0_param = 2,
  method = "splines",
  firth = T,
  spline_df = 4,
  max_iterations = 1000,
  min_iterations = 15,
  change_threshold = 0.1,
  epsilon = 0
)

Arguments

happi_results_boot	a happi results object for bootstrapping
h0_param	the column index in covariate that has beta=zero under the null
method	method for estimating f. Defaults to "splines" which fits a monotone spline with df determined by argument spline_df; "isotone" for isotonic regression fit
firth	use firth penalty? Default is TRUE.
spline_df	degrees of freedom (in addition to intercept) to use in monotone spline fit; default 3
max_iterations	the maximum number of EM steps that the algorithm will run for
min_iterations	the minimum number of EM steps that the algorithm will run for
change_threshold	algorithm will terminate early if the likelihood changes by this percentage or less for 5 iterations in a row for both the alternative and the null
epsilon	probability of observing a gene when it should be absent; probability between 0 and 1

Value

test statistic for one bootstrap iteration

statdivlab/happi documentation built on April 19, 2024, 2:04 a.m.