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-"
)
```

# denim <img src="man/figures/logo.svg" align="right" width="120" />

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An R package for building and simulating deterministic compartmental models with memory.

## Installation

You can install denim from CRAN with:

``` r
install.packages("denim")
```

Or install the development version of denim from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("thinhong/denim")
```

## Example

This is a basic example to illustrate the specification of a simple SIR model, which contains three compartments susceptible (S), infected (I) and recovered (R). The recovery probabilities of infected individuals are gamma distributed in this example:

```{r example}
library(denim)

transitions <- denim_dsl({
  S -> I = beta * S * I / N
  I -> R = d_gamma(rate = 1/3, shape = 2)
})

parameters <- c(
  beta = 1.2,
  N = 1000
)

initialValues <- c(
  S = 999, 
  I = 1, 
  R = 0
)

simulationDuration <- 20
timeStep <- 0.01

mod <- sim(transitions = transitions, initialValues = initialValues, 
           parameters = parameters, simulationDuration = simulationDuration, 
           timeStep = timeStep)
```

The output is a data frame with 4 columns: `Time`, `S`, `I` and `R`

```{r}
head(mod)
```

We can plot the output with:

```{r example-plot, dpi=300, fig.width=5}
plot(mod, ylim = c(1, 1000))
```