Calculate Log Likelihood without Sex Differentiation — mhLogLikelihood_clipp

This function calculates the log likelihood for a set of parameters and data without considering sex differentiation using the clipp package.

Usage

mhLogLikelihood_clipp_noSex(
  paras,
  families,
  twins,
  max_age,
  baseline_data,
  prev,
  geno_freq,
  trans,
  BaselineNC,
  ncores
)

paras: Numeric vector, the parameters for the Weibull distribution and scaling factors. Should contain in order: gamma, delta, given_median, given_first_quartile.
families: Data frame, containing pedigree information with columns for 'age', 'aff' (affection status), and 'geno' (genotype).
twins: Information on monozygous twins or triplets in the pedigrees.
max_age: Integer, maximum age considered in the analysis.
baseline_data: Numeric vector, baseline risk data for each age.
prev: Numeric, prevalence of the risk allele in the population.
geno_freq: Numeric vector, represents the frequency of the risk type and its complement in the population.
trans: Numeric matrix, transition matrix that defines the probabilities of allele transmission from parents to offspring.
BaselineNC: Logical, indicates if non-carrier penetrance should be based on the baseline data or the calculated non-carrier penetrance.
ncores: Integer, number of cores to use for parallel computation.

Numeric, the calculated log likelihood.

Details about the clipp package and methods can be found in the package documentation.