Consonance Property Checking for Hierarchical Testing

Implementation of consonance property validation for hierarchical multiple testing procedures. The consonance property ensures logical consistency: if a hypothesis is rejected, all hypotheses that logically imply it should also be rejectable. Essential for validating find_blocks() results and ensuring logical coherence.

Usage

check_consonance_property(
  node_dat,
  tracker,
  rejection_column = "testable",
  alpha = 0.05
)

Arguments

node_dat

Node data with test results

tracker

Node tracker with hierarchy structure

rejection_column

Column name containing rejection decisions

alpha

Type I error rate used for testing

Value

List with consonance check results and recommendations

References

Goeman, J. J., & Solari, A. (2011). Multiple testing for exploratory research. Statistical science, 26(4), 584-597.

Examples

if (FALSE) { # \dontrun{
# Check consonance of find_blocks results
# Requires dplyr package
data(example_dat, package = "manytestsr")
library(data.table)
library(dplyr)

# Prepare data
idat <- as.data.table(example_dat)
bdat <- idat %>%
  group_by(blockF) %>%
  summarize(
    nb = n(),
    pb = mean(trt),
    hwt = (nb / nrow(idat)) * (pb * (1 - pb)),
    .groups = "drop"
  ) %>%
  as.data.table()

# Run find_blocks
results <- find_blocks(
  idat = idat,
  bdat = bdat,
  blockid = "blockF",
  splitfn = splitCluster,
  pfn = pOneway,
  fmla = Y1 ~ trtF | blockF,
  splitby = "hwt",
  parallel = "no",
  maxtest = 20,
  trace = FALSE
)

# Check consonance of the testable decisions
consonance_check <- check_consonance_property(
  node_dat = results$node_dat,
  tracker = results$node_tracker, # Assuming tracker is available
  rejection_column = "testable",
  alpha = 0.05
)

# Examine consonance results
if (consonance_check$is_consonant) {
  cat("The hierarchical testing procedure is consonant.\n")
} else {
  cat("Found consonance violations:\n")
  for (i in seq_along(consonance_check$violations)) {
    violation <- consonance_check$violations[[i]]
    cat("-", violation$violation_description, "\n")
  }

  # Print violation analysis
  analysis <- consonance_check$violation_analysis
  cat("\nViolation Analysis:\n")
  cat("Total violations:", analysis$total_violations, "\n")
  cat("Severity level:", analysis$severity, "\n")
  cat("Affected nodes:", paste(analysis$affected_nodes, collapse = ", "), "\n")
}

# Apply consonance correction if needed
if (!consonance_check$is_consonant) {
  cat("\nApplying consonance correction...\n")

  corrected_results <- apply_consonance_correction(
    node_dat = results$node_dat,
    tracker = results$node_tracker,
    rejection_column = "testable",
    correction_method = "propagate_up"
  )

  # Check if correction worked
  corrected_check <- check_consonance_property(
    corrected_results,
    results$node_tracker,
    "testable_consonant"
  )

  if (corrected_check$is_consonant) {
    cat("Consonance correction successful.\n")
  } else {
    cat("Additional corrections may be needed.\n")
  }
}

# Compare original and corrected rejection counts
original_rejections <- sum(results$node_dat$testable, na.rm = TRUE)
if (exists("corrected_results")) {
  corrected_rejections <- sum(corrected_results$testable_consonant, na.rm = TRUE)
  cat("Original rejections:", original_rejections, "\n")
  cat("Corrected rejections:", corrected_rejections, "\n")
}
} # }