-
Notifications
You must be signed in to change notification settings - Fork 2
/
README.Rmd
61 lines (48 loc) · 1.88 KB
/
README.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# site <img src="man/figures/Site.png" align="right" width=30% height=30% />
<!-- badges: start -->
[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
[![R-CMD-check](https://github.com/mrc-ide/site/workflows/R-CMD-check/badge.svg)](https://github.com/mrc-ide/site/actions)
<!-- badges: end -->
Site acts as a translational layer between a site file and malariasimulation:
🌍 ➡️ 📉
The site file is the file storing all of the context specific information for a site,
such as historical intervention coverage, seasonality, vectors etc. To simulate
a given site, we must convert this information into an input parameter list for
malaria simulation. That is what site is here to do!
If we have a correctly configured site file `example_site`, then all we need to
do is create the parameter list and pass that to malariasimulation to run:
```{r, eval=FALSE}
site <- subset_site(example_site, example_site$eir[1,])
site_par <- site_parameters(
interventions = site$interventions,
demography = site$demography,
vectors = site$vectors$vector_species,
seasonality = site$seasonality$seasonality_parameters,
eir = site$eir$eir,
overrides = list(
human_population = 1000
)
)
site_sim <- malariasimulation::run_simulation(
timesteps = site_par$timesteps,
parameters = site_par
)
```
## Installation
You can install the development version of site from [GitHub](https://github.com/) with:
``` r
# install.packages("devtools")
devtools::install_github("mrc-ide/site")
```