Patherit: an R-package for estimating the heritability of pathogen traits

Pathogen traits, such as the virulence of an infection, can vary significantly between patients. A major challenge is to measure the extent to which genetic differences between infecting strains explain the observed variation of the trait. This is quantified by the trait’s broad-sense heritability, \(H^2\). The patherit R-package allows to compare various estimators of pathogen trait heritability in data simulated using the toyepidemic R-package, and in real epidemiological data.

The following methods are available:

  1. Direct heritability estimator, \(R_{adj}^2\), for data with full genetic and phenotype knowledge.
  2. Donor recipient regression slope, b, and intra-class correlation, \(r_A\), for transmission couple data;
  3. Several phylogenetic methods including ANOVA in phylogenetic pairs (PP) and closest phylogenetic pairs (CPP), the phylogenetic heritability estimated using the PMM and the POUMM.

Installing the package

You can install the most recent version of the package from github:

devtools::install_github(repo="venelin/patherit")

Using the package

For using the package, read the package Get started guide.

Package source-code

The package source-code is available on github.

Package web-page

Check-out the package web-page for the latest news and further documentation.