validate_baseline_data: Validate Baseline Penetrance Data

In penetrance: Methods for Penetrance Estimation in Family-Based Studies

Validate Baseline Penetrance Data

Description

This function validates baseline penetrance data to ensure it represents age-specific probabilities rather than cumulative risk. It checks for monotonicity and whether the sum exceeds 1, both of which suggest the data may be cumulative rather than age-specific.

Usage

validate_baseline_data(
  baseline_data,
  sex_specific = TRUE,
  param_name = "baseline_data",
  tolerance = 1e-10
)

Arguments

baseline_data	The baseline data to validate. Can be: A data frame with 'Male' and 'Female' columns (when sex_specific = TRUE) A numeric vector (when sex_specific = FALSE) A single-column data frame (when sex_specific = FALSE)
sex_specific	Logical, indicating whether the data is sex-specific. Default is TRUE.
param_name	Character string specifying the parameter name (for messages). Default is "baseline_data".
tolerance	Numeric value for checking strict monotonicity (to account for floating point precision). Default is 1e-10.

Details

The function performs the following checks:

• For monotonicity: If values are strictly non-decreasing (monotonically increasing), this suggests cumulative risk rather than age-specific probabilities. A warning is issued.

• For sum > 1: If the sum of all probabilities exceeds 1, this is problematic because these should be age-specific probabilities. A warning is issued.

• Individual values must be between 0 and 1 (probabilities)

• No NA or infinite values are allowed

Age-specific baseline risk represents the probability of developing disease at each specific age, while cumulative risk represents the total probability up to that age. For proper penetrance estimation, age-specific (not cumulative) risk should be used.

Value

Logical value TRUE if validation passes (with possible warnings), otherwise stops with an error.

Examples

# Valid age-specific data (varies, not monotone)
age_specific <- c(0.001, 0.002, 0.003, 0.002, 0.004, 0.003, 0.005)
validate_baseline_data(age_specific, sex_specific = FALSE)

# Valid sex-specific data
baseline_df <- data.frame(
  Male = c(0.001, 0.002, 0.001, 0.003),
  Female = c(0.002, 0.003, 0.002, 0.004)
)
validate_baseline_data(baseline_df, sex_specific = TRUE)

## Not run: 
# Will trigger warnings
# Monotone increasing (suggests cumulative risk)
cumulative <- c(0.001, 0.002, 0.003, 0.004, 0.005)
validate_baseline_data(cumulative, sex_specific = FALSE)

# Sum greater than 1
high_values <- rep(0.1, 15)  # sum = 1.5
validate_baseline_data(high_values, sex_specific = FALSE)

# Invalid data
invalid_data <- c(0.001, -0.002, 0.003)  # Negative value
validate_baseline_data(invalid_data, sex_specific = FALSE)

## End(Not run)

penetrance documentation built on Sept. 9, 2026, 1:07 a.m.