README.Rmd

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output: github_document
---

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

# CRTspat

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[`CRTspat`](https://thomasasmith.github.io/index.html) is an R-package to provide easily accessible R functions for design and analysis of cluster randomized trials (CRTs), where geographically structured spillover is anticipated and where geolocations are available. It includes functions for analysing baseline data, for defining clusters by algorithm, for power and sample size calculation, and for analysis of trial outcomes. It is designed to function with outcomes that are proportions, count data, or continuous variables.

The package was developed with CRTs of malaria interventions in mind, where the spillover is assumed to arise as a result of mosquito movement, with mosquito dispersal approximated with a simple diffusion model. This does not preclude its use in other fields of research. The anticipated use cases are described in the vignettes (articles) 

The package builds on the work of [Multerer *et al.* (2021a)](https://trialsjournal.biomedcentral.com/articles/10.1186/s13063-021-05543-8), [Multerer *et al.* (2021b)](https://malariajournal.biomedcentral.com/articles/10.1186/s12936-021-03924-7) and
 [Anaya-Izquierdo & Alexander(2021)](https://onlinelibrary.wiley.com/doi/full/10.1111/biom.13316).

## Code of Conduct

Please note that the CRTspat project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). 
By contributing to this project, you agree to abide by its terms.

## Installation

`CRTspat` is on [CRAN](https://CRAN.R-project.org/package=CRTspat) and 
on [github](https://github.com/ThomasASmith/CRTspat/). It can be installed from CRAN or using:

```{r, eval=F, echo=T}
install.packages("devtools")
library(devtools)
install_github("thomasasmith/CRTspat")
```

Markov chain Monte Carlo analysis using `CRTspat` also requires installation of [JAGS](https://mcmc-jags.sourceforge.io/)