Man pages for alan-turing-institute/network-comparison
An implementation of the NetEMD alignment-free network distance measure

adaptive_breaksGenerate a set of breaks that attempt to be evenly spaced...
area_between_dhist_ecmfsCalculate area between two discrete histogram empirical...
area_between_offset_ecmfsArea between two offset Empirical Cumulative Mass Functions...
as_smoothed_dhistSet dhist smoothing
as_unsmoothed_dhistRemove dhist smoothing
binned_densities_adaptivebinned_densities_adaptive
cost_matrixInter-bin cost matrix from bin centres
count_graphlets_egoEgo-network graphlet counts
count_graphlets_for_graphCount total number of graphlets in a graph
count_graphlets_per_nodeCount graphlets for each node in a graph
count_graphlet_tuplesFor each graphlet calculate the number of possible sets of k...
count_graphlet_tuples_egoRun count_graphlet_tuples across pre-computed ego networks.
count_orbits_per_nodeCount graphlet orbits for each node in a graph
counts_from_observationsCount number of occurences
cross_comparison_specGenerate a cross-comparison specification
cross_comp_to_matrixConvert a pair-wise cross-comparison into a matrix format
density_binned_countsUsed to calculate aggregated graphlet counts for each density...
density_binned_counts_gpCalculate expected counts in density bins using the geometric...
density_from_countsCalculate edge density for a single graph.
dhistDiscrete histogram constructor
dhist_ecmfGenerate interpolating empirical cumulative mass function...
dhist_from_obsDiscrete histogram from observations
dhist_from_obs_slowDiscrete histogram from observations (Pure R slow version)
dhist_mean_locationCalculate mean location for a discrete histogram
dhist_stdCalculate standard deviation of a discrete histogram
dhist_varianceCalculate variance of a discrete histogram
ecmf_knotsGet "knots" for discrete histogram empirical cumulative mass...
ego_network_densityCalculate ego network edge densities.
ego_to_graphlet_countsego_to_graphlet_counts
emdEarth Mover's Distance (EMD)
emd_csEarth Mover's Distance (EMD) using the difference of...
emd_fast_no_smoothingCompute Earth Mover's Distance (EMD) between two Empirical...
emd_lpEarth Mover's Distance (EMD) using linear programming (LP)
equals-.dhistCompare dhists
exp_counts_bin_gpINTERNAL FUNCTION - DO NOT CALL DIRECTLY Used by...
gddGraphlet-based degree distributions (GDDs)
gdd_for_all_graphsLoad all graphs in a directory and calculates their...
graph_features_to_histogramsConvert a matrix of node level features to a "discrete...
graphlet_ids_for_sizeGraphlet IDs for size
graphlet_keyGraphlet key
graph_to_indexed_edgesInteger index edge list from igraph
harmonise_dhist_locationsHarmonise a pair of discrete histograms to share a common set...
indexed_edges_to_graphGraph from integer index edge list
interval_indexBin values into intervals based on the provided breaks
is_dhistCheck if an object is a 'dhist' discrete histogram
is_numeric_vector_1dCheck if 1D numeric vector
make_named_ego_graphGet ego-networks for a graph as a named list
mean_centre_dhistCentre a discrete histogram around its mean location
mean_density_binned_graphlet_countsmean_density_binned_graphlet_counts
min_emdMinimum Earth Mover's Distance (EMD)
min_emd_exhaustiveMinimum Earth Mover's Distance (EMD) using exhaustive search
min_emd_optimiseMinimum Earth Mover's Distance (EMD) using optimiser search
min_emd_optimise_fastMinimum Earth Mover's Distance (EMD) using fast optimiser...
netdisNetdis - for one graphlet size
netdis_centred_graphlet_countsnetdis_centred_graphlet_counts
netdis_const_expected_countsCreate matrix of constant value to use as expected counts.
netdis_expected_countsnetdis_expected_counts
netdis_expected_counts_egonetdis_expected_counts_ego INTERNAL FUNCTION - Do not call...
netdis_many_to_manyCompute any of the Netdis variants between all graph pairs.
netdis_one_to_manyNetdis comparisons between one graph and many other graphs.
netdis_one_to_oneNetdis between two graphs
netdis.plotHeatmap of Netdis many-to-many comparisons
netdis_subtract_exp_countsnetdis_subtract_exp_counts
netdis_uptokNetdis - for all graphlet sizes up to max_graphlet_size
netemd_many_to_manyNetEMDs between all graph pairs using provided Graphlet-based...
netemd_one_to_oneNetEMD Network Earth Mover's Distance between a pair of...
netemd.plotHeatmap of NetEmd many-to-many comparisons
netemd_single_pairInternal function to compute the minimum Earth Mover's...
normalise_dhist_massNormalise a discrete histogram to unit mass
normalise_dhist_varianceNormalise a discrete histogram to unit variance
orbit_keyOrbit key
orbit_to_graphlet_countsOrbit to graphlet counts
read_simple_graphRead a graph from file, simplifying as requested
read_simple_graphsRead all graphs in a directory, simplifying as requested
scale_graphlet_countDivide graphlet counts by pre-computed scaling factor from...
scale_graphlet_counts_egoScale graphlet counts for an ego network by the n choose k...
shift_dhistShift discrete histogram
shift_to_next_alignmentMinimum shift to next alignment of two location vectors
simplify_graphSimplify an igraph
single_density_binFor case where don't want to use binning, return a single bin...
sort_dhistSort discrete histogram
virusppiProtein-protein interaction (PPI) networks for 5...
worldtradesubWorld trade networks from 1985–2014
zeros_to_onesReplace zero values in a vector with ones. Used by...
alan-turing-institute/network-comparison documentation built on June 7, 2022, 10:41 p.m.