Implementation of LT-FH++

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Documentation for package ‘LTFHPlus’ version 2.1.1

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construct_covmat Constructing a covariance matrix for a variable number of phenotypes
construct_covmat_multi Constructing a covariance matrix for multiple phenotypes
construct_covmat_single Constructing a covariance matrix for a single phenotype
convert_age_to_cir Convert age to cumulative incidence rate
convert_age_to_thresh Convert age to threshold
convert_cir_to_age Convert cumulative incidence rate to age
convert_format Attempts to convert the list entry input format to a long format
convert_liability_to_aoo Convert liability to age of onset
convert_observed_to_liability_scale Convert the heritability on the observed scale to that on the liability scale
correct_positive_definite Positive definite matrices
estimate_gen_liability_ltfh Estimate genetic liability similar to LT-FH
estimate_liability Estimating the genetic or full liability for a variable number of phenotypes
estimate_liability_multi Estimating the genetic or full liability for multiple phenotypes
estimate_liability_single Estimating the genetic or full liability
get_all_combs construct all combinations of input vector
get_kinship Construct kinship matrix from graph
get_relatedness Relatedness between a pair of family members
graph_based_covariance_construction Constructing covariance matrix from local family graph
graph_based_covariance_construction_multi Constructing covariance matrix from local family graph for multi trait analysis
prepare_graph Construct graph from register information
prepare_LTFHPlus_input Prepares input for 'estimate_liability'
rtmvnorm.gibbs Gibbs Sampler for the truncated multivariate normal distribution
simulate_under_LTM Simulate under the liability threshold model.
simulate_under_LTM_multi Simulate under the liability threshold model (multiple phenotypes).
simulate_under_LTM_single Simulate under the liability threshold model (single phenotype).
truncated_normal_cdf CDF for truncated normal distribution.