nestor: Network inference from Species counTs with missing actORs.

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.

Installation

EMtree dependency

nestor uses functions from the R package EMtree which development version is available from GitHub

devtools::install_github("Rmomal/EMtree")

CRAN dependencies

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 with:

devtools::install_github("Rmomal/nestor")