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.