Function reference • EMtree

Main user functions
`EMtree()`	Core computing function
`ResampleEMtree()`	Resampling procedure for edges probability
`StATS()`	Stability Approach to Threshold Selection
`freq_selec()`	Computes edges selection frequency after resampling procedure
`data_from_scratch()`	Simulates data under the PLN model with control on the dependency structure
Tools
`Laplacian()`	Compute a matrix Laplacian
`SumTree()`	Summing over trees (Matrix Tree Theorem)
`EdgeProba()`	Computing edge probabilities
`Kirshner()`	Computing edge probabilities using Kirshner (07) formula
`ToSym()`	Makes a symmetric matrix from the vector made of its upper triangular part
`ToVec()`	Makes a vector from the upper triangular part of a symmetric matrix
Computing functions
`FitBeta()`	Update the beta weights according to the gradient ascent
`Meila()`	Computing the M matrix
`Psi_alpha()`	Choice of alpha for a numerically stable psi matrix
For simulations
`generator_PLN()`	Simulate count data under the Poisson log-Normal model
`generator_graph()`	Simulate several types of graphs
`generator_param()`	Generate simulation parameters from a graph adjacency matrix
`SimCluster()`	Simulates a cluster graph
`SpannTree()`	Simulates a spanning tree graph from `vegan`package
`erdos()`	Simulates an Erdös-Renyi graph
Visualization
`draw_network()`	Plots a network

Reference