README.Rmd

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output: github_document
---

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knitr::opts_chunk$set(
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```

# CommunitySim

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CommunitySim simulates an ecological community, such as a microbiome using Lotka-Volterra based models. In particular, dynamics of species are simulated assuming a third species can influence the intensity of pairwise interactions, an assumption referred to as a higher-order interaction.

<center>
![](man/figures/summar.png){width=20%}
</center>

## Introduction

Lotka-Volterra describes the change of abundance of species relating to the abundance of all members in the community:

![](man/figures/lv.png){width=20%}

where alpha_i is species i's growth rate without the influence from other species; b_ij is the impact of other species on the growth of i, on a per unit basis.

The higher-order interaction states that a third species can not only interact with other species in a pairwise manner, but also influence the intensity of existing pairwise interactions in the community, which is modeled by b_ij:

![](man/figures/glv.png){width=20%}

Here the pairwise interaction intensity is modeled as a flat rate modified by the abundance of third species, x_k. 

With varying interaction intensity and initial abundance of species, the change in abundance of the community over time can be studied by solving the coupled ODEs. This package provides a simulation of above stated parameters, and a solver for the coupled ODEs.

## Installation

You can install the development version from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("yuan-yin-truly/CommunitySim")
```

## How to use

Please refer to the vignette at `doc/CommunitySim.html` or `doc/CommunitySim.pdf`.