Skip to content

Commit

Permalink
minor edit.
Browse files Browse the repository at this point in the history
  • Loading branch information
Venelin Mitov committed Jan 6, 2018
1 parent c2dba44 commit e3a4ed9
Show file tree
Hide file tree
Showing 3 changed files with 3 additions and 3 deletions.
2 changes: 1 addition & 1 deletion README.Rmd
Expand Up @@ -17,7 +17,7 @@ knitr::opts_chunk$set(
This package provides methods for simulating the evolution of pathogen traits. The simulation method assumes a classical additive model for a trait in which the trait-value is formed as a sum of single-locus and epistatic effects from the pathogen genotype, the host immune system type and a white noise term representing the combination of unknown non-heritable factors such as unknown pathogen and host immune system loci, host environment and measurement error. It is assumed that the genotype of the pathogen can mutate during an infection as a result of neutral genetic drift or within-host selection for an optimal trait-value. At the between-host level various events, such as transmission to susceptible hosts, diagnosis and immunity are simulated according to a Susceptible-Infected-Recovered (SIR) epidemiological model. The rates at which these events occur as well as contact rates between infected and susceptible hosts can be specified as constants or as functions of the pathogen trait. The resulting epidemic is represented as a `data.table` and a rooted phylogenetic tree (a phylo object). The data contains the history of within- and between- host events. For a further introduction to the toy epidemiological model, we refer the reader to [@Mitov:2016kd].

# Using the package
For using the package, read the package [User Guide](https://venelin.github.io/toyepidemic/articles/UserGuide.html).
For using the package, read the package [Get started](https://venelin.github.io/toyepidemic/articles/UserGuide.html) guide.

# Installing the package
You can install the most recent version of the package from github:
Expand Down
2 changes: 1 addition & 1 deletion README.md
Expand Up @@ -8,7 +8,7 @@ This package provides methods for simulating the evolution of pathogen traits. T
Using the package
=================

For using the package, read the package [User Guide](https://venelin.github.io/toyepidemic/articles/UserGuide.html).
For using the package, read the package [Get started](https://venelin.github.io/toyepidemic/articles/UserGuide.html) guide.

Installing the package
======================
Expand Down
2 changes: 1 addition & 1 deletion docs/index.html

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

0 comments on commit e3a4ed9

Please sign in to comment.