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

aal116Coordinates for data from the AAl116 atlas
aal2.120Coordinates for data from the AAL2 atlas
aal2.94Coordinates for data from the AAL2 atlas
aal90Coordinates for data from the AAl90 atlas
analysis_random_graphsPerform an analysis with random graphs for brain MRI data
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
bg_to_mediateConvert brainGraph results to "mediate" object
brainGraph_bootBootstrapping for global graph measures
brainGraph_GLMFit linear models at each vertex of a graph
brainGraph_GLM_designCreate a design matrix for linear model analysis
brainGraph_GLM_fitFit linear models for t contrasts
brainGraph_initInitialize variables for further use in brainGraph
brainGraph_mediateMediation analysis with brain graph measures as mediator...
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
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
destrieuxCoordinates for data from the Destrieux atlas
destrieux.scgmCoordinates for data from the Destrieux atlas
dkCoordinates for data from the Desikan-Killiany atlas
dk.scgmCoordinates for data from the Desikan-Killiany atlas
dktCoordinates for data from the Desikan-Killiany-Tourville...
dkt.scgmCoordinates for data from the Desikan-Killiany-Tourville...
dosenbach160Coordinates for data from the Dosenbach160 atlas
edge_asymmetryCalculate an asymmetry index based on edge counts
efficiencyCalculate graph global, local, or nodal efficiency
get_lm_varsGet some variables for LM
get.residLinear model residuals in structural covariance networks
glm_helpersHelper function to set-up for GLM analyses
hoa112Coordinates for data from Harvard-Oxford atlas
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
mtpcMulti-threshold permutation correction
NBSNetwork-based statistic for brain MRI data
partitionPartition a design matrix into columns of interest and...
plot.bg_GLMPlot GLM diagnostics for a brain network
plot.brainGraphPlot a brain graph with a specific spatial layout
plot.brainGraph_bootPlot bootstrap output of global graph measures across...
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.brainGraph_permutePlot results from permutation testing
plot.brainGraph_residsPlot model residuals for each brain region
plot_corr_matPlot a correlation matrix
plot_globalPlot global graph measures across densities
plot.mtpcPlot statistics from an MTPC analysis
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_graphsSimulate N random graphs w/ same clustering and degree...
randomiseHelper function to setup for randomise
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
summary.bg_GLMPrint a summary from brainGraph_GLM analysis
summary.bg_mediatePrint a summary from a brainGraph mediation analysis
summary.brainGraphPrint a summary of a brainGraph object
summary.brainGraph_permutePrint a summary from a permutation analysis
symmetrize_matsCreate a symmetric matrix
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 May 5, 2018, 2:14 a.m.