Implementation of LT-FH++

---

Documentation for package ‘LTFHPlus’ version 2.1.4

• DESCRIPTION file.
• Package NEWS.

Help Pages

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
fixSexCoding	Fixing sex coding in trio info
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
graph_to_trio	Convert from igraph to trio information
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.