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-",
  out.width = "80%",fig.align="center",
  warning=FALSE
)
library(magrittr)
library(ggplot2)
library(tibble)
library(EMtree)
```

# nestor: Network inference from Species counTs with missing actORs.

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> `nestor` is an R package for the inference of species interaction networks from their observed abundances, while accounting for possible unobserved missing actors in the data. It is an implementation of the tree-based VEM algorithm described in the preprint [http://arxiv.org/abs/2007.14299](http://arxiv.org/abs/2007.14299).

## Installation

### EMtree dependency

`nestor` uses functions from the R package `EMtree` which development version is available from [GitHub](https://github.com/) 
```{r,eval=FALSE}
devtools::install_github("Rmomal/EMtree")
```

### CRAN dependencies

```{r,eval=FALSE}
required_CRAN <- c("utils", "stats", "ROCR","graphics", "mvtnorm", "parallel", 
                   "gridExtra", "reshape2"  ,"ggplot2", "magrittr", "dplyr", 
                   "tidyr", "tibble", "blockmodels", "mclust", "PLNmodels")
not_installed_CRAN <- setdiff(required_CRAN, rownames(installed.packages()))
if (length(not_installed_CRAN) > 0) install.packages(not_installed_CRAN)
```

### Installation of `nestor`
You can install the development version from [GitHub](https://github.com/) with:

```{r, eval=FALSE}
devtools::install_github("Rmomal/nestor")
```