Implementation of LT-FH++.

Emil M. Pedersen 01/02/2024

LTFHPlus

LTFHPlus implements the method LT-FH++, an extension of the liability threshold model conditioned on family history (LT-FH). It accounts for information such as right censoring, age of onset, sex, and cohort effects, and allows for flexible family structures.

LT-FH++ can be used to estimate an individual’s genetic component of the full liability, the full liability or both by accounting for the family history and population prevalences. It utilises an efficient Gibbs sampler, which is implemented with Rcpp and is highly scaleable. A detailed description of the liability threshold model conditioned on family history, age of onset and sex can be found here.

Installation

You can install LTFHPlus by:

devtools::install_github("EmilMiP/LTFHPlus")

or for the CRAN version:

install.packages("LTFHPlus")

Documentation

Documentation for the different functions, as well as examples of how to use them, can be found on this pkgdown website.

Changes to 2.0

The most important change to version 2.0 is a more flexible covariance matrix construction, and the corresponding update to the input. The change to the covariance matrix allows users to include family members with far more flexibility, allowing users to completely exclude parents, use paternal/maternal half-siblings, grandparents, and more.