Man pages for brainGraph
Graph Theory Analysis of Brain MRI Data
| apply_thresholds | Threshold additional set of matrices |
| atlas_helpers | Atlas helper functions |
| attributes | Set graph, vertex, and edge attributes common in MRI analyses |
| auc_diff | Difference in the area-under-the-curve of two vectors |
| Bootstrapping | Bootstrapping for global graph measures |
| brain_atlases | Coordinates for data from brain atlases |
| brainGraph | Default options for brainGraph |
| brainGraphList | Create a list of brainGraph graphs |
| brainGraph-methods | brainGraph generic methods |
| brainGraph_permute | Permutation test for group difference of graph measures |
| centr_betw_comm | Calculate communicability betweenness centrality |
| centr_lev | Calculate a vertex's leverage centrality |
| check_attributes | Check for vertex or edge attributes |
| choose.edges | Select edges for re-wiring |
| coeff_var | Calculate coefficient of variation |
| communicability | Calculate communicability |
| contract_brainGraph | Contract graph vertices based on brain lobe and hemisphere |
| cor.diff.test | Calculate the p-value for differences in correlation... |
| correlation_matrices | Calculate correlation matrix and threshold |
| count_edges | Count number of edges of a brain graph |
| create_mats | Create connection matrices for tractography or fMRI data |
| data_tables | Create a data table with graph global and vertex measures |
| delete_all_attr | Delete all attributes of a graph |
| dir2files | Return a vector of filenames based on a directory name or... |
| edge_asymmetry | Calculate an asymmetry index based on edge counts |
| efficiency | Calculate graph global, local, or nodal efficiency |
| get_rand_attrs | Convenience function to get attributes for lists of random... |
| glm | Fit General Linear Models at each vertex of a graph |
| glm_brainGraphList | Create a graph list with GLM-specific attributes |
| glm_design | Create a design matrix for linear model analysis |
| glm_fit | Fit design matrices to one or multiple outcomes |
| glm_graph_plots | Plot a graph with results from GLM-based analyses |
| glm_helpers | Helper functions to set-up for GLM analyses |
| glm_influence | Influence measures for a bg_GLM object |
| glm_info | Extract basic information from a bg_GLM object |
| glm_model_select | Model selection for bg_GLM objects |
| glm_stats | Extract model fit statistics from a bg_GLM object |
| hubness | Calculate vertex hubness |
| import_scn | Import data for structural connectivity analysis |
| individ_contrib | Approaches to estimate individual network contribution |
| inverse | Calculate the inverse of the cross product of a design matrix |
| make_auc_brainGraph | Calculate the AUC across densities of given attributes |
| make_brainGraph | Create a brainGraph object |
| make_ego_brainGraph | Create a graph of the union of multiple vertex neighborhoods |
| make_intersection_brainGraph | Create the intersection of graphs based on a logical... |
| matrix_utils | Matrix/array utility functions |
| mean_distance_wt | Calculate weighted shortest path lengths |
| mediation | Mediation analysis with brain graph measures as mediator... |
| mtpc | Multi-threshold permutation correction |
| NBS | Network-based statistic for brain MRI data |
| pad_zeros | Test if an object is a character vector of numbers |
| plot.brainGraph | Plot a brain graph with a specific spatial layout |
| plot_brainGraph_gui | GUI for plotting graphs overlaid on an MNI152 image or in a... |
| plot.brainGraphList | Plot a brainGraphList and write to PDF |
| plot_brainGraph_multi | Save PNG of one or three views for all graphs in a... |
| plot_global | Plot global graph measures across densities |
| plot_rich_norm | Plot normalized rich club coefficients against degree... |
| plot_vertex_measures | Plot vertex-level graph measures at a single density or... |
| plot_volumetric | Plot group distributions of volumetric measures for a given... |
| random_graphs | Perform an analysis with random graphs for brain MRI data |
| randomise | GLM non-parametric permutation testing |
| rename_levels | Rename the levels of global metrics in a data.table |
| residuals | Linear model residuals in structural covariance networks |
| rich_club | Rich club calculations |
| rich_club_attrs | Assign graph attributes based on rich-club analysis |
| robustness | Analysis of network robustness |
| s_core | Calculate the s-core of a network |
| set_graph_colors | Color graph vertices and edges |
| small.world | Calculate graph small-worldness |
| spatial_dist | Calculate Euclidean distance of edges and vertices |
| subset_graph | Subset graphs based on a given logical condition |
| update_fs_names | Update column names in a Freesurfer table |
| utils | Utility functions |
| vertex_roles | Gateway coefficient, participation coefficient, and... |
| vif.bg_GLM | Variance inflation factors for 'bg_GLM' objects |
| vulnerability | Calculate graph vulnerability |
| write_brainnet | Write files to be used for visualization with BrainNet Viewer |
