Man pages for cwatson/brainGraph
Graph Theory Analysis of Brain MRI Data

aalCoordinates for data from the AAL-based atlases
apply_thresholdsThreshold additional set of matrices
args_as_listConvert arguments into a single list
auc_diffDifference in the area-under-the-curve of two vectors
brainGraph_bootBootstrapping for global graph measures
brainGraph_GLM_fitFit linear models for t contrasts
brainGraph_initInitialize variables for further use in brainGraph
brainGraph_permutePermutation test for group difference of graph measures
brainsuiteCoordinates for data from BrainSuite atlas
centr_betw_commCalculate communicability betweenness centrality
centr_levCalculate a vertex's leverage centrality
check_degreeCheck for presence of a degree attribute
check_strengthCheck for presence of a strength attribute
check_weightsCheck for edge weights
choose.edgesSelect edges for re-wiring.
coeff_varCalculate coefficient of variation
color_vertices_edgesColor graph vertices and edges
communicabilityCalculate communicability
contract_brainGraphContract graph vertices based on brain lobe and hemisphere
cor.diff.testCalculate the p-value for differences in correlation...
corr.matrixCalculate correlation matrix and threshold
count_edgesCount number of edges of a brain graph
craddock200Coordinates for data from the Craddock200 atlas
create_matsCreate connection matrices for tractography or fMRI data
data_tablesCreate a data table with graph global and vertex measures
delete_all_attrDelete all attributes of a graph
dosenbach160Coordinates for data from the Dosenbach160 atlas
edge_asymmetryCalculate an asymmetry index based on edge counts
efficiencyCalculate graph global, local, or nodal efficiency
freesurfer_atlasesCoordinates for data from Freesurfer atlases
get_lm_varsGet some variables for LM
glmFit linear models at each vertex of a graph
glm_designCreate a design matrix for linear model analysis
glm_helpersHelper function to set-up for GLM analyses
hoa112Coordinates for data from Harvard-Oxford atlas
hubnessCalculate vertex hubness
individ_contribApproaches to estimate individual network contribution
is.brainGraphDetermine whether x is a brainGraph object
lpba40Coordinates for data from the LONI probabilistic brain atlas
make_brainGraphCreate a brainGraph object
make_ego_brainGraphCreate a graph of the union of multiple vertex neighborhoods
make_empty_brainGraphCreate an empty graph with attributes for brainGraph
make_glm_brainGraphCreate a graph with GLM-specific attributes
make_intersection_brainGraphCreate the intersection of graphs based on a logical...
make_mediate_brainGraphCreate a graph with mediation-specific attributes
make_nbs_brainGraphCreate a graph with NBS-specific attributes
mediationMediation analysis with brain graph measures as mediator...
mtpcMulti-threshold permutation correction
NBSNetwork-based statistic for brain MRI data
partitionPartition a design matrix into columns of interest and...
plot.brainGraphPlot a brain graph with a specific spatial layout
plot.brainGraph_GLMPlot a graph with results from brainGraph_GLM
plot_brainGraph_guiGUI for plotting graphs overlaid on an MNI152 image or in a...
plot_brainGraph_listWrite PNG files for a list of graphs
plot.brainGraph_mediatePlot a graph with results from a mediation analysis
plot.brainGraph_mtpcPlot a graph with results from MTPC
plot_brainGraph_multiSave PNG of three views of a brain graph
plot.brainGraph_NBSPlot a graph with results from the network-based statistic
plot_corr_matPlot a correlation matrix
plot_globalPlot global graph measures across densities
plot_rich_normPlot normalized rich club coefficients against degree...
plot_vertex_measuresPlot vertex-level graph measures at a single density or...
plot_volumetricPlot group distributions of volumetric measures for a given...
random_graphsPerform an analysis with random graphs for brain MRI data
randomiseHelper function to setup for randomise
residualsLinear model residuals in structural covariance networks
rich_clubRich club calculations
rich_club_attrsAssign graph attributes based on rich-club analysis
robustnessAnalysis of network robustness
rotationApply a rotation matrix to a set of points
rstudent_matCalculate studentized residuals with matrix input
s_coreCalculate the s-core of a network
set_brainGraph_attrSet graph, vertex, and edge attributes common in MRI analyses
small.worldCalculate graph small-worldness
spatial_distCalculate Euclidean distance of edges and vertices
subset_graphSubset graphs based on a given logical condition
symmetrize_matsCreate a symmetric matrix
symm_meanSymmetrize a matrix with the mean of off-diagonal elements
update_brainGraph_guiFunction to dynamically plot a graph
vec.transformTransform a vector to have a different range
vertex_rolesGateway coefficient, participation coefficient, and...
vulnerabilityCalculate graph vulnerability
write_brainnetWrite files to be used for visualization with BrainNet Viewer
xfm.weightsTransform edge weights
cwatson/brainGraph documentation built on Sept. 6, 2018, 2:32 p.m.