Package index

Network Structure Inference Methods

ensemble_ggm()

Resampling-based Markov Network

ensemble_cgbn()

Resampling-based conditional Gaussian Bayesian Network

consensus_net_ggm()

Create consensus network of resampling-based Markov network

consensus_net_cgbn()

Create consensus network of resampling-based conditional Gaussian Bayesian network

resample()

Perform data resampling

resample_cluster()

Perform data resampling from correlated data

matrix_p_adjust()

Perform adjustments of p-values on a p x p matrix

upper_tri_to_matrix()

Reconstruct the symmetric matrix from upper triangular vector

Graphlet-based Methods

gdvm_gcm()

Find graphlet degree vector (GDV) of each vertex and graphlet correlation matrix of the given network

signed_gdvm_gcm()

Function to count signed graphlets

gdv_distance()

Find the graphlet degree distance between two vertices

intra_gdv_distance()

Pair-wise GDV distance

paired_gdv_distance()

Compute Paired Graphlet Degree Vector (GDV) Distances

gcm_distance()

Distance between two Graphlet Correlation Matrices

Community Detection Methods

community_detection()

Perform community detection on a network

remove_isolated()

Remove isolated nodes from a network

remove_small_community()

Remove small communities in a network

Centrality Methods

centrality()

Compute essential centrality of a network

Differential Connectivity Methods

null_ggm()

Differential connectivity nulls via permutation/bootstrap + GGM

permutation_diffanal()

Permutation for differential connectivity analysis

bootstrap_diffanal()

Bootstrap for differential connectivity analysis (pooled bootstrap)

diff_centrality()

Differential centrality between two observed networks

diff_gdv()

GDV distance-based Differential Connectivity Analysis

Plot Methods

plot_cn()

Plot Consensus Network

Simulation Methods

model_er()

Simulate network via erdos-renyi model

model_pa()

Simulate network via preferential attachment model

model_mpa()

Simulate network via modular preferential attachment model

model_sbm()

Simulate network via stochastic block model

model_sw()

Simulate network via small world model

model_sim()

Simulate multivariate Gaussian data for an undirected graph model

sim_fam_data()

Simulate family-based correlated data

Data Objects

toy_er

Toy undirected network generated by ER-model

toy_cgbn

Toy dataset of mixture data type

toy_load

Toy dataset from LOAD study

Miscellaneous

distinct_colors()

Distinct colors for large categorical datasets

normalize_range()

Normalize values between a given range

colorize()

Colorize numerical values

colorize_community()

Assign unique color to each community

ggempty()

An empty ggplot

jaccard_similarity()

Calculate the Jaccard similarity between vectors or matrices

capture_all()

Silently evaluate an expression while returning its value