brainGraph3.1.1 package

Threshold additional set of matrices

Atlas helper functions

Set graph, vertex, and edge attributes common in MRI analyses

Difference in the area-under-the-curve of two vectors

Bootstrapping for global graph measures

Coordinates for data from brain atlases

Permutation test for group difference of graph measures

brainGraph generic methods

Default options for brainGraph

Create a list of brainGraph graphs

Calculate communicability betweenness centrality

Calculate a vertex's leverage centrality

Check for vertex or edge attributes

Select edges for re-wiring

Calculate coefficient of variation

Calculate communicability

Contract graph vertices based on brain lobe and hemisphere

Calculate the p-value for differences in correlation coefficients

Calculate correlation matrix and threshold

Count number of edges of a brain graph

Create connection matrices for tractography or fMRI data

Create a data table with graph global and vertex measures

Delete all attributes of a graph

Return a vector of filenames based on a directory name or options list

Calculate an asymmetry index based on edge counts

Calculate graph global, local, or nodal efficiency

Convenience function to get attributes for lists of random graphs

Create a graph list with GLM-specific attributes

Create a design matrix for linear model analysis

Fit design matrices to one or multiple outcomes

Plot a graph with results from GLM-based analyses

Helper functions to set-up for GLM analyses

Influence measures for a bg_GLM object

Extract basic information from a bg_GLM object

Model selection for bg_GLM objects

Extract model fit statistics from a bg_GLM object

Fit General Linear Models at each vertex of a graph

Calculate vertex hubness

Import data for structural connectivity analysis

Approaches to estimate individual network contribution

Calculate the inverse of the cross product of a design matrix

Calculate the AUC across densities of given attributes

Create a brainGraph object

Create a graph of the union of multiple vertex neighborhoods

Create the intersection of graphs based on a logical condition

Matrix/array utility functions

Calculate weighted shortest path lengths

Mediation analysis with brain graph measures as mediator variables

Multi-threshold permutation correction

Network-based statistic for brain MRI data

Test if an object is a character vector of numbers

Save PNG of one or three views for all graphs in a brainGraphList

Plot global graph measures across densities

Plot normalized rich club coefficients against degree threshold

Plot vertex-level graph measures at a single density or threshold

Plot group distributions of volumetric measures for a given brain regi...

Plot a brain graph with a specific spatial layout

Plot a brainGraphList and write to PDF

Perform an analysis with random graphs for brain MRI data

GLM non-parametric permutation testing

Rename the levels of global metrics in a data.table

Linear model residuals in structural covariance networks

Assign graph attributes based on rich-club analysis

Rich club calculations

Analysis of network robustness

Calculate the s-core of a network

Color graph vertices and edges

Calculate graph small-worldness

Calculate Euclidean distance of edges and vertices

Subset graphs based on a given logical condition

Update column names in a Freesurfer table

Utility functions

Gateway coefficient, participation coefficient, and within-mod degree ...

Variance inflation factors for bg_GLM objects

Calculate graph vulnerability

Write files to be used for visualization with BrainNet Viewer