This repository contains source and rendered output for epicontacts: Handling, Visualisation and Analysis of Epidemiological Contacts.
The manuscript is written in R Markdown, and can be found in epicontacts-paper.Rmd
... note that this is the only place you need to edit for narrative content. This file includes a mix of evaluated and unevaluated R code chunks, and uses the f1000_article
R Markdown latex template from BiocWorkflowTools. Figures were generated outside of the document and are included using standard Markdown syntax. If you are adding a new citation, add a BibTex version entry to biblio.bib
and inline reference.
To render the document, make sure you have the necessary packages installed ...
install.packages(c("rmarkdown", "epicontacts", "outbreaks"))
source("https://bioconductor.org/biocLite.R")
biocLite("BiocWorkflowTools")
... then from the root of the repository run rmarkdown::render("epicontacts-paper.Rmd")