Hierarchical (serial gatekeeping) Bonferroni procedure

Families are tested in order; if a family produces no rejections, subsequent families are blocked from testing. rmorie-specific stage-list return shape; no drop-in CRAN equivalent (gMCP covers the concept but with a different graphical API).

Usage

hierarchical_bonferroni(
  p_values_by_family,
  alpha = 0.05,
  propagate_alpha = TRUE
)

Arguments

p_values_by_family

List of numeric vectors, one per family.

alpha

Overall FWER level.

propagate_alpha

Not implemented. Alpha recycling between families would need a named procedure; what runs instead is that every family is tested at the full alpha and the gate closes on the first family with no rejection. Passing this argument explicitly warns, and alpha_propagated in the result is FALSE. Ignored; kept so the signature is stable across families (mirrors the Python reference).

Value

A morie_rich_result list with one stage entry per family and an overall_rejected logical vector.

Examples

res <- hierarchical_bonferroni(list(c(0.4, 0.5), c(0.001, 0.002)))
str(res)
#> List of 10
#>  $ title           : chr "Hierarchical Bonferroni Gatekeeping"
#>  $ call            : chr "families=2, alpha=0.0500"
#>  $ summary_lines   :List of 4
#>   ..$ Families      : int 2
#>   ..$ alpha         : num 0.05
#>   ..$ Total rejected: int 0
#>   ..$ Gate closed   : logi TRUE
#>  $ warnings        : chr(0) 
#>  $ interpretation  : chr "Serial gatekeeping across 2 famil(ies) with alpha=0.0500 yielded 0 total rejection(s). A downstream gate was cl"| __truncated__
#>  $ stages          :List of 2
#>   ..$ :List of 6
#>   .. ..$ family    : int 1
#>   .. ..$ n_tests   : int 2
#>   .. ..$ alpha_used: num 0.05
#>   .. ..$ n_rejected: int 0
#>   .. ..$ adjusted_p: num [1:2] 0.8 1
#>   .. ..$ rejected  : logi [1:2] FALSE FALSE
#>   ..$ :List of 6
#>   .. ..$ family    : int 2
#>   .. ..$ n_tests   : int 2
#>   .. ..$ alpha_used: num 0
#>   .. ..$ n_rejected: int 0
#>   .. ..$ adjusted_p: num [1:2] 1 1
#>   .. ..$ rejected  : logi [1:2] FALSE FALSE
#>  $ overall_rejected: logi [1:4] FALSE FALSE FALSE FALSE
#>  $ method          : chr "hierarchical_bonferroni"
#>  $ alpha           : num 0.05
#>  $ alpha_propagated: logi FALSE
#>  - attr(*, "class")= chr [1:3] "morie_multiple_testing_result" "morie_rich_result" "list"