brm_recenter_nuisance {brms.mmrm}

Recenter nuisance variables

Description

Change the center of a nuisance variable of an informative prior archetype.

Usage

brm_recenter_nuisance(data, nuisance, center)

Arguments

data

An informative prior archetype data frame output from brm_archetype_cells() or similar.

nuisance

Character of length 1, name of the nuisance column in the data to shift the center.

center

Numeric of length 1, value of the center to shift the column in nuisance. The affected column in the returned archetype data frame will look as if it were centered by this value to begin with.

Details

By "centering vector y at scalar x", we mean taking the difference z = y - x. If x is the mean, then mean(z) is 0. Informative prior archetypes center nuisance variables at their means so the parameters can be interpreted correctly for setting informative priors. This is appropriate most of the time, but sometimes it is better to center a column at a pre-specified scientifically meaningful fixed number. If you want a nuisance column to be centered at a fixed value other than its mean, use brm_recenter_nuisance() to shift the center. This function can handle any nuisance variable

Value

An informative prior archetype data frame with one of the variables re-centered.

Examples

set.seed(0L)
data <- brm_simulate_outline(
  n_group = 2,
  n_patient = 100,
  n_time = 4,
  rate_dropout = 0,
  rate_lapse = 0
) |>
  dplyr::mutate(response = rnorm(n = dplyr::n())) |>
  brm_data_change() |>
  brm_simulate_continuous(names = c("biomarker1", "biomarker2")) |>
  brm_simulate_categorical(
    names = c("status1", "status2"),
    levels = c("present", "absent")
  )
archetype <- brm_archetype_cells(data)
mean(archetype$nuisance_biomarker1) # after original centering
center <- mean(data$biomarker1)
center # original center, before the centering from brm_archetype_cells()
attr(archetype$nuisance_biomarker1, "brm_center") # original center
max(abs((data$biomarker1 - center) - archetype$nuisance_biomarker1))
# Re-center nuisance_biomarker1 at 0.75.
archetype <- brm_recenter_nuisance(
  data = archetype,
  nuisance = "nuisance_biomarker1",
  center = 0.75
)
attr(archetype$nuisance_biomarker1, "brm_center") # new center
mean(archetype$nuisance_biomarker1) # no longer equal to the center
# nuisance_biomarker1 is now as though we centered it at 0.75.
max(abs((data$biomarker1 - 0.75) - archetype$nuisance_biomarker1))