Graph Theory Analysis of Brain MRI Data

Documentation for package ‘brainGraph’ version 3.1.0

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A B C D E F G H I L M N P Q R S T V W X misc

Default options for brainGraph

-- A --

aal116	Coordinates for data from brain atlases
aal2.120	Coordinates for data from brain atlases
aal2.94	Coordinates for data from brain atlases
aal90	Coordinates for data from brain atlases
analysis_random_graphs	Perform an analysis with random graphs for brain MRI data
anova.bg_GLM	Extract model fit statistics from a bg_GLM object
aop	Approaches to estimate individual network contribution
apply_thresholds	Threshold additional set of matrices
as_atlas	Atlas helper functions
as_brainGraphList	Create a list of brainGraph graphs
Atlas Helpers	Atlas helper functions
Attributes	Set graph, vertex, and edge attributes common in MRI analyses

-- B --

bg_to_mediate	Mediation analysis with brain graph measures as mediator variables
Bootstrapping	Bootstrapping for global graph measures
Brain Atlases	Coordinates for data from brain atlases
brainGraph	Default options for brainGraph
brainGraph-methods	brainGraph generic methods
brainGraph-options	Default options for brainGraph
brainGraphList	Create a list of brainGraph graphs
brainGraph_boot	Bootstrapping for global graph measures
brainGraph_GLM	Fit General Linear Models at each vertex of a graph
brainGraph_GLM_design	Create a design matrix for linear model analysis
brainGraph_mediate	Mediation analysis with brain graph measures as mediator variables
brainGraph_permute	Permutation test for group difference of graph measures
brainnetome	Coordinates for data from brain atlases
brainsuite	Coordinates for data from brain atlases

-- C --

case.names.bg_GLM	Extract basic information from a bg_GLM object
case.names.brainGraph_resids	Linear model residuals in structural covariance networks
case.names.mtpc	Multi-threshold permutation correction
case.names.NBS	Network-based statistic for brain MRI data
centr_betw_comm	Calculate communicability betweenness centrality
centr_lev	Calculate a vertex's leverage centrality
check_sID	Test if an object is a character vector of numbers
coef.bg_GLM	Extract model fit statistics from a bg_GLM object
coeff_determ	Extract model fit statistics from a bg_GLM object
coeff_table	Extract model fit statistics from a bg_GLM object
coeff_var	Calculate coefficient of variation
coeff_var.default	Calculate coefficient of variation
colMax	Matrix/array utility functions
colMaxAbs	Matrix/array utility functions
colMin	Matrix/array utility functions
communicability	Calculate communicability
confint.bg_GLM	Extract model fit statistics from a bg_GLM object
contract_brainGraph	Contract graph vertices based on brain lobe and hemisphere
cooks.distance.bg_GLM	Influence measures for a bg_GLM object
cor.diff.test	Calculate the p-value for differences in correlation coefficients
corr.matrix	Calculate correlation matrix and threshold
Count Edges	Count number of edges of a brain graph
count_homologous	Count number of edges of a brain graph
count_inter	Count number of edges of a brain graph
covratio.bg_GLM	Influence measures for a bg_GLM object
craddock200	Coordinates for data from brain atlases
create_atlas	Atlas helper functions
create_mats	Create connection matrices for tractography or fMRI data
Creating_Graphs	Create a brainGraph object
Creating_Graphs_GLM	Create a graph list with GLM-specific attributes

-- D --

destrieux	Coordinates for data from brain atlases
destrieux.scgm	Coordinates for data from brain atlases
deviance.bg_GLM	Extract model fit statistics from a bg_GLM object
df.residual.bg_GLM	Extract model fit statistics from a bg_GLM object
df.residual.mtpc	Multi-threshold permutation correction
df.residual.NBS	Network-based statistic for brain MRI data
dfbeta.bg_GLM	Influence measures for a bg_GLM object
dfbetas.bg_GLM	Influence measures for a bg_GLM object
dffits.bg_GLM	Influence measures for a bg_GLM object
diag_sq	Matrix/array utility functions
dk	Coordinates for data from brain atlases
dk.scgm	Coordinates for data from brain atlases
dkt	Coordinates for data from brain atlases
dkt.scgm	Coordinates for data from brain atlases
dosenbach160	Coordinates for data from brain atlases

-- E --

edge_asymmetry	Calculate an asymmetry index based on edge counts
edge_spatial_dist	Calculate Euclidean distance of edges and vertices
efficiency	Calculate graph global, local, or nodal efficiency
Extract.brainGraphList	Create a list of brainGraph graphs
Extract.brainGraph_resids	Linear model residuals in structural covariance networks
Extract.corr_mats	Calculate correlation matrix and threshold
extractAIC.bg_GLM	Model selection for bg_GLM objects

-- F --

fastLmBG	Fit design matrices to one or multiple outcomes
fastLmBG_3d	Fit design matrices to one or multiple outcomes
fastLmBG_3dY	Fit design matrices to one or multiple outcomes
fastLmBG_3dY_1p	Fit design matrices to one or multiple outcomes
fastLmBG_f	Fit design matrices to one or multiple outcomes
fastLmBG_t	Fit design matrices to one or multiple outcomes
fitted.bg_GLM	Extract model fit statistics from a bg_GLM object
formula.bg_GLM	Extract basic information from a bg_GLM object
formula.mtpc	Multi-threshold permutation correction
formula.NBS	Network-based statistic for brain MRI data

-- G --

gateway_coeff	Gateway coefficient, participation coefficient, and within-mod degree z-score
get.resid	Linear model residuals in structural covariance networks
get_thresholds	Matrix/array utility functions
GLM	Fit General Linear Models at each vertex of a graph
GLM basic info	Extract basic information from a bg_GLM object
GLM design	Create a design matrix for linear model analysis
GLM fits	Fit design matrices to one or multiple outcomes
GLM influence measures	Influence measures for a bg_GLM object
GLM model selection	Model selection for bg_GLM objects
GLM statistics	Extract model fit statistics from a bg_GLM object
gordon333	Coordinates for data from brain atlases
Graph Data Tables	Create a data table with graph global and vertex measures
Graph Distances	Calculate Euclidean distance of edges and vertices
graph_attr_dt	Create a data table with graph global and vertex measures
groups.brainGraphList	brainGraph generic methods
groups.brainGraph_resids	Linear model residuals in structural covariance networks
groups.corr_mats	brainGraph generic methods
guess_atlas	Atlas helper functions

-- H --

hatvalues.bg_GLM	Influence measures for a bg_GLM object
hcp_mmp1.0	Coordinates for data from brain atlases
hoa112	Coordinates for data from brain atlases
hubness	Calculate vertex hubness

-- I --

import_scn	Import data for structural connectivity analysis
IndividualContributions	Approaches to estimate individual network contribution
influence.bg_GLM	Influence measures for a bg_GLM object
inv	Calculate the inverse of the cross product of a design matrix
inv.array	Calculate the inverse of the cross product of a design matrix
inv.list	Calculate the inverse of the cross product of a design matrix
inv.matrix	Calculate the inverse of the cross product of a design matrix
inv.qr	Calculate the inverse of the cross product of a design matrix
Inverse	Calculate the inverse of the cross product of a design matrix
is.brainGraph	Create a brainGraph object
is.brainGraphList	Create a list of brainGraph graphs
is_binary	Matrix/array utility functions

-- L --

labels.bg_GLM	Extract basic information from a bg_GLM object
labels.mtpc	Multi-threshold permutation correction
labels.NBS	Network-based statistic for brain MRI data
logLik.bg_GLM	Model selection for bg_GLM objects
loo	Approaches to estimate individual network contribution
lpba40	Coordinates for data from brain atlases

-- M --

make_auc_brainGraph	Calculate the AUC across densities of given attributes
make_brainGraph	Create a brainGraph object
make_brainGraph.bg_mediate	Create a brainGraph object
make_brainGraph.igraph	Create a brainGraph object
make_brainGraph.matrix	Create a brainGraph object
make_brainGraphList	Create a list of brainGraph graphs
make_brainGraphList.array	Create a list of brainGraph graphs
make_brainGraphList.bg_GLM	Create a graph list with GLM-specific attributes
make_brainGraphList.corr_mats	Create a list of brainGraph graphs
make_brainGraphList.mtpc	Create a graph list with GLM-specific attributes
make_brainGraphList.NBS	Create a graph list with GLM-specific attributes
make_ego_brainGraph	Create a graph of the union of multiple vertex neighborhoods
make_empty_brainGraph	Create a brainGraph object
make_intersection_brainGraph	Create the intersection of graphs based on a logical condition
Matrix utilities	Matrix/array utility functions
mean_distance_wt	Calculate weighted shortest path lengths
Mediation	Mediation analysis with brain graph measures as mediator variables
mtpc	Multi-threshold permutation correction

-- N --

NBS	Network-based statistic for brain MRI data
nobs.bg_GLM	Extract basic information from a bg_GLM object
nobs.brainGraphList	Create a list of brainGraph graphs
nobs.brainGraph_resids	Linear model residuals in structural covariance networks
nobs.mtpc	Multi-threshold permutation correction
nobs.NBS	Network-based statistic for brain MRI data
nregions	brainGraph generic methods
nregions.bg_GLM	Extract basic information from a bg_GLM object
nregions.brainGraph_resids	Linear model residuals in structural covariance networks
nregions.corr_mats	Calculate correlation matrix and threshold
nregions.mtpc	Multi-threshold permutation correction
nregions.NBS	Network-based statistic for brain MRI data

-- P --

pad_zeros	Test if an object is a character vector of numbers
partition	GLM non-parametric permutation testing
part_coeff	Gateway coefficient, participation coefficient, and within-mod degree z-score
pinv	Calculate the inverse of the cross product of a design matrix
plot.bg_GLM	Fit General Linear Models at each vertex of a graph
plot.brainGraph	Plot a brain graph with a specific spatial layout
plot.brainGraphList	Plot a brainGraphList and write to PDF
plot.brainGraph_boot	Bootstrapping for global graph measures
plot.brainGraph_GLM	Plot a graph with results from GLM-based analyses
plot.brainGraph_mediate	Plot a graph with results from GLM-based analyses
plot.brainGraph_mtpc	Plot a graph with results from GLM-based analyses
plot.brainGraph_NBS	Plot a graph with results from GLM-based analyses
plot.brainGraph_permute	Permutation test for group difference of graph measures
plot.brainGraph_resids	Linear model residuals in structural covariance networks
plot.corr_mats	Calculate correlation matrix and threshold
plot.IC	Approaches to estimate individual network contribution
plot.mtpc	Multi-threshold permutation correction
Plotting GLM graphs	Plot a graph with results from GLM-based analyses
plot_brainGraph_multi	Save PNG of one or three views for all graphs in a brainGraphList
plot_global	Plot global graph measures across densities
plot_rich_norm	Plot normalized rich club coefficients against degree threshold
plot_vertex_measures	Plot vertex-level graph measures at a single density or threshold
plot_volumetric	Plot group distributions of volumetric measures for a given brain region
power264	Coordinates for data from brain atlases
print.bg_GLM	Fit General Linear Models at each vertex of a graph
print.brainGraphList	Create a list of brainGraph graphs

-- Q --

qr.array	Matrix/array utility functions
qr_Q2	Matrix/array utility functions
qr_R2	Matrix/array utility functions

-- R --

Random Graphs	Perform an analysis with random graphs for brain MRI data
randomise	GLM non-parametric permutation testing
randomise_3d	GLM non-parametric permutation testing
region.names	brainGraph generic methods
region.names.bg_GLM	Extract basic information from a bg_GLM object
region.names.brainGraph_resids	Linear model residuals in structural covariance networks
region.names.corr_mats	Calculate correlation matrix and threshold
region.names.data.table	brainGraph generic methods
region.names.mtpc	Multi-threshold permutation correction
Residuals	Linear model residuals in structural covariance networks
residuals.bg_GLM	Extract model fit statistics from a bg_GLM object
Rich Club	Rich club calculations
rich_club_all	Rich club calculations
rich_club_attrs	Assign graph attributes based on rich-club analysis
rich_club_coeff	Rich club calculations
rich_club_norm	Rich club calculations
rich_core	Rich club calculations
robustness	Analysis of network robustness
rstandard.bg_GLM	Influence measures for a bg_GLM object
rstudent.bg_GLM	Influence measures for a bg_GLM object

-- S --

set_brainGraph_attr	Set graph, vertex, and edge attributes common in MRI analyses
sigma.bg_GLM	Extract model fit statistics from a bg_GLM object
sim.rand.graph.clust	Perform an analysis with random graphs for brain MRI data
sim.rand.graph.hqs	Perform an analysis with random graphs for brain MRI data
sim.rand.graph.par	Perform an analysis with random graphs for brain MRI data
slicer	Save PNG of one or three views for all graphs in a brainGraphList
small.world	Calculate graph small-worldness
summary.bg_GLM	Fit General Linear Models at each vertex of a graph
summary.bg_mediate	Mediation analysis with brain graph measures as mediator variables
summary.brainGraph	Create a brainGraph object
summary.brainGraph_boot	Bootstrapping for global graph measures
summary.brainGraph_permute	Permutation test for group difference of graph measures
summary.brainGraph_resids	Linear model residuals in structural covariance networks
summary.IC	Approaches to estimate individual network contribution
summary.mtpc	Multi-threshold permutation correction
summary.NBS	Network-based statistic for brain MRI data
symmetrize	Matrix/array utility functions
symmetrize.array	Matrix/array utility functions
symmetrize.matrix	Matrix/array utility functions
symm_mean	Matrix/array utility functions
s_core	Calculate the s-core of a network

-- T --

terms.bg_GLM	Extract basic information from a bg_GLM object
terms.mtpc	Multi-threshold permutation correction
terms.NBS	Network-based statistic for brain MRI data

-- V --

variable.names.bg_GLM	Extract basic information from a bg_GLM object
variable.names.mtpc	Multi-threshold permutation correction
variable.names.NBS	Network-based statistic for brain MRI data
vcov.bg_GLM	Extract model fit statistics from a bg_GLM object
Vertex Roles	Gateway coefficient, participation coefficient, and within-mod degree z-score
vertex_attr_dt	Create a data table with graph global and vertex measures
vertex_spatial_dist	Calculate Euclidean distance of edges and vertices
vif.bg_GLM	Variance inflation factors for 'bg_GLM' objects
vulnerability	Calculate graph vulnerability

-- W --

within_module_deg_z_score	Gateway coefficient, participation coefficient, and within-mod degree z-score
write_brainnet	Write files to be used for visualization with BrainNet Viewer

-- X --

xfm.weights

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

-- misc --

[.bg_GLM	Fit General Linear Models at each vertex of a graph
[.brainGraphList	Create a list of brainGraph graphs
[.brainGraph_resids	Linear model residuals in structural covariance networks
[.corr_mats	Calculate correlation matrix and threshold