README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# phylepic

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Phylepic contains tools for visualisations that are useful for genomic epidemiology
of pathogens, designed for a public health setting.

## Installation

You can install phylepic like so:

``` r
# CRAN release
install.packages('phylepic')

# development version
install.packages('phylepic', repos = c('https://cidmp-ph.r-universe.dev', 'https://cloud.r-project.org'))
```

## Example

This is an example of a very minimal phylepic chart.

```{r example, fig.width=7, fig.height=4, eval = F}
library(ape)
library(phylepic)

tree <- read.tree(text = "((D:0.3,C:0.4):0.5,B:0.1,A:0.2);")
metadata <- data.frame(
  ID = c("A", "B", "C", "D"),
  date = as.Date(c("2024-01-10", "2024-01-12", "2024-01-21", "2024-01-23")),
  country = factor(c("Australia", "Australia", NA, "New Zealand"))
)

phylepic(tree, metadata, ID, date) |> plot()
```

Refer to [the package vignette](https://cidm-ph.github.io/phylepic/articles/phylepic.html) for a more complete example.


## Citation

See `citation("phylepic")`.

Suster CJE, Watt AE, Wang Q, Chen SC, Kok J, Sintchenko V (2024).
“Combined visualization of genomic and epidemiological data for outbreaks.”
_Epidemiology & Infection_ 152: e110. [doi:10.1017/S0950268824001092](https://doi.org/10.1017/S0950268824001092),