Imputes missing ages in family-based data using a combination of Weibull distributions for affected individuals and empirical distributions for unaffected individuals. The function can perform both sex-specific and non-sex-specific imputations.
Usage
imputeAges(
data,
na_indices,
baseline_male = NULL,
baseline_female = NULL,
alpha_male = NULL,
beta_male = NULL,
delta_male = NULL,
alpha_female = NULL,
beta_female = NULL,
delta_female = NULL,
baseline = NULL,
alpha = NULL,
beta = NULL,
delta = NULL,
max_age,
sex_specific = TRUE,
max_attempts = 100,
geno_freq,
trans,
lik
)Arguments
- data
A data frame containing family-based data with columns: family, individual, father, mother, sex, aff, age, geno, and isProband
- na_indices
Vector of indices where ages need to be imputed
- baseline_male, baseline_female
Data frames containing baseline age distributions for males/females
- alpha_male, alpha_female
Shape parameters for male/female Weibull distributions
- beta_male, beta_female
Scale parameters for male/female Weibull distributions
- delta_male, delta_female
Location parameters for male/female Weibull distributions
- baseline
Data frame containing overall baseline age distribution (non-sex-specific)
- alpha, beta, delta
Overall Weibull parameters (non-sex-specific)
- max_age
Maximum allowable age
- sex_specific
Logical; whether to use sex-specific parameters
- max_attempts
Maximum number of attempts for generating valid ages
- geno_freq
Vector of genotype frequencies
- trans
Transmission probabilities
- lik
Likelihood matrix