incomplete_loglik: Function for calculating incomplete log likelihood

In statdivlab/happi: a hierarchical approach to pangenomics inference

Function for calculating incomplete log likelihood

Description

Function for calculating incomplete log likelihood

Usage

incomplete_loglik(
  xbeta,
  ff,
  firth = TRUE,
  outcome = outcome,
  epsilon = epsilon,
  covariate
)

Arguments

xbeta	my fitted betas matrix multiplied by covariate
ff	my estimated f's
firth	use Firth penalty? default: TRUE
outcome	length-n vector; this is the vector of a target gene's presence/absence; should be coded as 0 or 1
epsilon	probability of observing a gene when it should be absent; probability between 0 and 1
covariate	n x p matrix; this is the matrix for the primary predictor/covariate of interest

Value

incomplete log-likelihood value

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