Man pages for alan-turing-institute/network-comparison
An implementation of the NetEMD alignment-free network distance measure
| adaptive_breaks | Generate a set of breaks that attempt to be evenly spaced... |
| area_between_dhist_ecmfs | Calculate area between two discrete histogram empirical... |
| area_between_offset_ecmfs | Area between two offset Empirical Cumulative Mass Functions... |
| as_smoothed_dhist | Set dhist smoothing |
| as_unsmoothed_dhist | Remove dhist smoothing |
| binned_densities_adaptive | binned_densities_adaptive |
| cost_matrix | Inter-bin cost matrix from bin centres |
| count_graphlets_ego | Ego-network graphlet counts |
| count_graphlets_for_graph | Count total number of graphlets in a graph |
| count_graphlets_per_node | Count graphlets for each node in a graph |
| count_graphlet_tuples | For each graphlet calculate the number of possible sets of k... |
| count_graphlet_tuples_ego | Run count_graphlet_tuples across pre-computed ego networks. |
| count_orbits_per_node | Count graphlet orbits for each node in a graph |
| counts_from_observations | Count number of occurences |
| cross_comparison_spec | Generate a cross-comparison specification |
| cross_comp_to_matrix | Convert a pair-wise cross-comparison into a matrix format |
| density_binned_counts | Used to calculate aggregated graphlet counts for each density... |
| density_binned_counts_gp | Calculate expected counts in density bins using the geometric... |
| density_from_counts | Calculate edge density for a single graph. |
| dhist | Discrete histogram constructor |
| dhist_ecmf | Generate interpolating empirical cumulative mass function... |
| dhist_from_obs | Discrete histogram from observations |
| dhist_from_obs_slow | Discrete histogram from observations (Pure R slow version) |
| dhist_mean_location | Calculate mean location for a discrete histogram |
| dhist_std | Calculate standard deviation of a discrete histogram |
| dhist_variance | Calculate variance of a discrete histogram |
| ecmf_knots | Get "knots" for discrete histogram empirical cumulative mass... |
| ego_network_density | Calculate ego network edge densities. |
| ego_to_graphlet_counts | ego_to_graphlet_counts |
| emd | Earth Mover's Distance (EMD) |
| emd_cs | Earth Mover's Distance (EMD) using the difference of... |
| emd_fast_no_smoothing | Compute Earth Mover's Distance (EMD) between two Empirical... |
| emd_lp | Earth Mover's Distance (EMD) using linear programming (LP) |
| equals-.dhist | Compare dhists |
| exp_counts_bin_gp | INTERNAL FUNCTION - DO NOT CALL DIRECTLY Used by... |
| gdd | Graphlet-based degree distributions (GDDs) |
| gdd_for_all_graphs | Load all graphs in a directory and calculates their... |
| graph_features_to_histograms | Convert a matrix of node level features to a "discrete... |
| graphlet_ids_for_size | Graphlet IDs for size |
| graphlet_key | Graphlet key |
| graph_to_indexed_edges | Integer index edge list from igraph |
| harmonise_dhist_locations | Harmonise a pair of discrete histograms to share a common set... |
| indexed_edges_to_graph | Graph from integer index edge list |
| interval_index | Bin values into intervals based on the provided breaks |
| is_dhist | Check if an object is a 'dhist' discrete histogram |
| is_numeric_vector_1d | Check if 1D numeric vector |
| make_named_ego_graph | Get ego-networks for a graph as a named list |
| mean_centre_dhist | Centre a discrete histogram around its mean location |
| mean_density_binned_graphlet_counts | mean_density_binned_graphlet_counts |
| min_emd | Minimum Earth Mover's Distance (EMD) |
| min_emd_exhaustive | Minimum Earth Mover's Distance (EMD) using exhaustive search |
| min_emd_optimise | Minimum Earth Mover's Distance (EMD) using optimiser search |
| min_emd_optimise_fast | Minimum Earth Mover's Distance (EMD) using fast optimiser... |
| netdis | Netdis - for one graphlet size |
| netdis_centred_graphlet_counts | netdis_centred_graphlet_counts |
| netdis_const_expected_counts | Create matrix of constant value to use as expected counts. |
| netdis_expected_counts | netdis_expected_counts |
| netdis_expected_counts_ego | netdis_expected_counts_ego INTERNAL FUNCTION - Do not call... |
| netdis_many_to_many | Compute any of the Netdis variants between all graph pairs. |
| netdis_one_to_many | Netdis comparisons between one graph and many other graphs. |
| netdis_one_to_one | Netdis between two graphs |
| netdis.plot | Heatmap of Netdis many-to-many comparisons |
| netdis_subtract_exp_counts | netdis_subtract_exp_counts |
| netdis_uptok | Netdis - for all graphlet sizes up to max_graphlet_size |
| netemd_many_to_many | NetEMDs between all graph pairs using provided Graphlet-based... |
| netemd_one_to_one | NetEMD Network Earth Mover's Distance between a pair of... |
| netemd.plot | Heatmap of NetEmd many-to-many comparisons |
| netemd_single_pair | Internal function to compute the minimum Earth Mover's... |
| normalise_dhist_mass | Normalise a discrete histogram to unit mass |
| normalise_dhist_variance | Normalise a discrete histogram to unit variance |
| orbit_key | Orbit key |
| orbit_to_graphlet_counts | Orbit to graphlet counts |
| read_simple_graph | Read a graph from file, simplifying as requested |
| read_simple_graphs | Read all graphs in a directory, simplifying as requested |
| scale_graphlet_count | Divide graphlet counts by pre-computed scaling factor from... |
| scale_graphlet_counts_ego | Scale graphlet counts for an ego network by the n choose k... |
| shift_dhist | Shift discrete histogram |
| shift_to_next_alignment | Minimum shift to next alignment of two location vectors |
| simplify_graph | Simplify an igraph |
| single_density_bin | For case where don't want to use binning, return a single bin... |
| sort_dhist | Sort discrete histogram |
| virusppi | Protein-protein interaction (PPI) networks for 5... |
| worldtradesub | World trade networks from 1985–2014 |
| zeros_to_ones | Replace zero values in a vector with ones. Used by... |
