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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# hypatia
<!-- badges: start -->
[![R build status](https://github.com/mrc-ide/hypatia/workflows/R-CMD-check/badge.svg)](https://github.com/mrc-ide/hypatia/actions)
[![CodeFactor](https://www.codefactor.io/repository/github/mrc-ide/hypatia/badge)](https://www.codefactor.io/repository/github/mrc-ide/hypatia)
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<!-- badges: end -->
The goal of hypatia is to enable SQUIRE to be run on an individual basis rather than aggregate
## Installation
``` r
install_github('mrc-ide/individual')
library(individual)
```
## Example
Get parameters from SQUIRE
```{r, simulation, echo = FALSE}
R0 <- 2
time_period <- 1000
tt_contact_matrix <- 0
contact_matrix_set <- squire::contact_matrices[[1]]
pop <- hypatia:::get_population("Afghanistan")
psq <- hypatia:::get_parameters(
population = pop$n,
R0 = R0,
time_period = time_period,
contact_matrix_set = contact_matrix_set,
tt_contact_matrix = tt_contact_matrix
)
```
## License
MIT © Imperial College of Science, Technology and Medicine