Emil M. Pedersen 01/02/2024
LTFHPlus implements the method LT-FH++, an extension of the liabilitythreshold model conditioned on family history(LT-FH). Itaccounts for information such as right censoring, age of onset, sex, andcohort effects, and allows for flexible family structures.
LT-FH++ can be used to estimate an individual’s genetic component ofthe full liability, the full liability or both by accounting for thefamily history and population prevalences. It utilises an efficientGibbs sampler, which is implemented withRcpp and is highly scaleable. Adetailed description of the liability threshold model conditioned onfamily history, age of onset and sex can be foundhere.
You can install LTFHPlus by:
devtools::install_github("EmilMiP/LTFHPlus")or for the CRAN version:
install.packages("LTFHPlus")
Documentation for the different functions, as well as examples of howto use them, can be found onthis pkgdown website.
The most important change to version 2.0 is a more flexiblecovariance matrix construction, and the corresponding update to theinput. The change to the covariance matrix allows users to includefamily members with far more flexibility, allowing users to completelyexclude parents, use paternal/maternal half-siblings, grandparents, andmore.