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Marginalize conditional cumulative incidences

Source: R/marginalize_psi_dx.R
marginalize_psi_dx_t0.Rd

Averages day- and covariate-specific cumulative incidences from compute_psi_dx_t0() to produce overall cumulative incidences under each exposure. By default, performs a simple average. If weights are provided for in gp_list, performs a weighted average.

Usage

marginalize_psi_dx_t0(psi_dx, gp_list = NULL, show_intermediates = FALSE)

Arguments

psi_dx

A data frame with conditional risk predictions containing:

  • <covariates>: all covariate columns

  • <exposure_time>: vaccination day column

  • psi_0_dx: cumulative incidence under no vaccine,\(\psi_0(t_0; d, x)\)

  • psi_1_dx: cumulative incidence under vaccine,\(\psi_1(t_0; d, x)\)

Typically output from compute_psi_dx_t0().

gp_list

A list with two data frames:

  • g_weights Data frame of covariate-conditional exposure-day probabilities \(g(d \mid x)\). Must include:

    • group_id: covariate group identifier

    • <exposure_time>: exposure time variable

    • prob_g: probability of exposure time given the covariates

    • all variables in covariates

  • p_weights Data frame of covariate probabilities \(p(x)\). Must include:

  • group_id: covariate group identifier

  • prob_p: marginal probability of each covariate group

  • all variables in covariates

Default is NULL in which case each row of psi_dx gets equal weight.

show_intermediates

Logical that only applies when gp_list is not NULL; when FALSE(default), the function performs marginalization in a single step and returns only the overall cumulative incidences \eqn{\bar{\psi}_0(t_0)} and \eqn{\bar{\psi}_1(t_0)}. WhenTRUE“, performs the two-step marginalization (first over days \(d\), then covariate groups \(x\)) and returns intermediate group-level results \(\psi_v(t_0; x)\).

Value

When show_intermediates = FALSE, a named numeric vector with two elements:

  • cuminc_0: Overall cumulative incidence under no exposure

  • cuminc_1: Overall cumulative incidence under exposure

When show_intermediates = TRUE, a list containing both overall results (as a vector) and group-specific results (as a data frame).

See also