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%"
)
```

# coiaf <a href='https://bailey-lab.github.io/coiaf/'><img src='man/figures/logo.png' align="right" height="139" /></a>

```{r logo, eval = F, include = F}
# Code for logo. To run, use the R package `hexSticker`
sticker("man/figures/logo_background.jpg",
  package = "coiaf",
  filename = "man/figures/logo2.png",
  s_x = 1, s_y = 1, s_width = 1.7,
  p_size = 12, p_x = 0.95, p_y = 1.5, p_color = "#fdead4",
  h_color = "#93a448", h_fill = "#75d8c3",
  white_around_sticker = T, dpi = 500
)
```

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## Introduction
In malaria, individuals are often infected with different parasite strains, with
the complexity of infection (COI) giving the number of genetically different
parasite strains in an individual. Changes in the mean COI in a population have
been shown to be informative of changes in transmission intensity with a number
of probabilistic likelihood and Bayesian models now developed to estimate COI.
However, rapid, direct measures based on heterozygosity or *FwS* have not been
directly related to the COI. This package features two rapid, direct measures
for characterizing polyclonal infections.

## Installation

::: .pkgdown-release
```{r, eval = FALSE}
# Install most recent released version
devtools::install_github("bailey-lab/coiaf@v0.1.2")
```
:::

::: .pkgdown-devel
```{r, eval = FALSE}
# Install development version
devtools::install_github("bailey-lab/coiaf")
```
:::

## Usage
In order to run real data, please refer to the Articles drop-down menu. Several
articles detail how the algorithm works, how data is simulated to test the
algorithm, and, importantly, how to run real data. A short example of running
real data is included and outlines the necessary data structure and the commands
to run.