Files in alan-turing-institute/network-comparison
An implementation of the NetEMD alignment-free network distance measure
.Rbuildignore
.github/workflows/build.yml
.github/workflows/pkgdown.yml
.gitignore
DESCRIPTION
LICENSE
Meta/vignette.rds
NAMESPACE
R/PlottingFunctions.R
R/RcppExports.R
R/catch-routine-registration.R
R/data.R
R/dhist.R
R/emd.R
R/graph_binning.R
R/measures_net_dis.R
R/measures_net_emd.R
R/net_emd_speed_benchmark.R
R/netdist_package.R
R/orca_interface.R
R/utility_functions.R
README.md
data-raw/virus.R
data/virusppi.rda
data/worldtradesub.rda
doc/V-Menu.R
doc/V-Menu.Rmd
doc/V-Menu.html
doc/default_pairwise_usage.R
doc/default_pairwise_usage.Rmd
doc/default_pairwise_usage.html
doc/dendrogram_example_net_dis.R
doc/dendrogram_example_net_dis.Rmd
doc/dendrogram_example_net_dis.html
doc/dendrogram_example_net_emd.R
doc/dendrogram_example_net_emd.Rmd
doc/dendrogram_example_net_emd.html
doc/netdis_2graphs_polya-aeppli.R
doc/netdis_2graphs_polya-aeppli.Rmd
doc/netdis_2graphs_polya-aeppli.html
doc/netdis_customisations.R
doc/netdis_customisations.Rmd
doc/netdis_customisations.html
doc/netdis_pairwise_comparisons.R
doc/netdis_pairwise_comparisons.Rmd
doc/netdis_pairwise_comparisons.html
doc/quickstart_netdis_2graphs.R
doc/quickstart_netdis_2graphs.Rmd
doc/quickstart_netdis_2graphs.html
inst/extdata/VRPINS/EBV.txt
inst/extdata/VRPINS/ECL.txt
inst/extdata/VRPINS/HSV-1.txt
inst/extdata/VRPINS/KSHV.txt
inst/extdata/VRPINS/VZV.txt
inst/extdata/random/BA_1250_10_1
inst/extdata/random/BA_1250_10_2
inst/extdata/random/BA_1250_10_3
inst/extdata/random/BA_5000_20_1
inst/extdata/random/BA_5000_20_2
inst/extdata/random/BA_5000_20_3
inst/extdata/random/DD1_1250_10_1
inst/extdata/random/DD1_1250_10_2
inst/extdata/random/DD1_1250_10_3
inst/extdata/random/DD1_5000_20_1
inst/extdata/random/DD1_5000_20_2
inst/extdata/random/DD1_5000_20_3
inst/extdata/random/DD2_1250_10_1
inst/extdata/random/DD2_1250_10_2
inst/extdata/random/DD2_1250_10_3
inst/extdata/random/DD2_5000_20_1
inst/extdata/random/DD2_5000_20_2
inst/extdata/random/DD2_5000_20_3
inst/extdata/random/ERDD_1250_10_1
inst/extdata/random/ERDD_1250_10_2
inst/extdata/random/ERDD_1250_10_3
inst/extdata/random/ERDD_5000_20_1
inst/extdata/random/ERDD_5000_20_2
inst/extdata/random/ERDD_5000_20_3
inst/extdata/random/ER_1250_10_1
inst/extdata/random/ER_1250_10_2
inst/extdata/random/ER_1250_10_3
inst/extdata/random/ER_5000_20_1
inst/extdata/random/ER_5000_20_2
inst/extdata/random/ER_5000_20_3
inst/extdata/random/GDD3D_1250_10_1
inst/extdata/random/GDD3D_1250_10_2
inst/extdata/random/GDD3D_1250_10_3
inst/extdata/random/GDD3D_5000_20_1
inst/extdata/random/GDD3D_5000_20_2
inst/extdata/random/GDD3D_5000_20_3
inst/extdata/random/Geo3D_1250_10_1
inst/extdata/random/Geo3D_1250_10_2
inst/extdata/random/Geo3D_1250_10_3
inst/extdata/random/Geo3D_5000_20_1
inst/extdata/random/Geo3D_5000_20_2
inst/extdata/random/Geo3D_5000_20_3
inst/extdata/random/WS_1250_10_1
inst/extdata/random/WS_1250_10_2
inst/extdata/random/WS_1250_10_3
inst/extdata/random/WS_5000_20_1
inst/extdata/random/WS_5000_20_2
inst/extdata/random/WS_5000_20_3
man/adaptive_breaks.Rd
man/area_between_dhist_ecmfs.Rd
man/area_between_offset_ecmfs.Rd
man/as_smoothed_dhist.Rd
man/as_unsmoothed_dhist.Rd
man/binned_densities_adaptive.Rd
man/cost_matrix.Rd
man/count_graphlet_tuples.Rd
man/count_graphlet_tuples_ego.Rd
man/count_graphlets_ego.Rd
man/count_graphlets_for_graph.Rd
man/count_graphlets_per_node.Rd
man/count_orbits_per_node.Rd
man/counts_from_observations.Rd
man/cross_comp_to_matrix.Rd
man/cross_comparison_spec.Rd
man/density_binned_counts.Rd
man/density_binned_counts_gp.Rd
man/density_from_counts.Rd
man/dhist.Rd
man/dhist_ecmf.Rd
man/dhist_from_obs.Rd
man/dhist_from_obs_slow.Rd
man/dhist_mean_location.Rd
man/dhist_std.Rd
man/dhist_variance.Rd
man/ecmf_knots.Rd
man/ego_network_density.Rd
man/ego_to_graphlet_counts.Rd
man/emd.Rd
man/emd_cs.Rd
man/emd_fast_no_smoothing.Rd
man/emd_lp.Rd
man/equals-.dhist.Rd
man/exp_counts_bin_gp.Rd
man/gdd.Rd
man/gdd_for_all_graphs.Rd
man/graph_features_to_histograms.Rd
man/graph_to_indexed_edges.Rd
man/graphlet_ids_for_size.Rd
man/graphlet_key.Rd
man/harmonise_dhist_locations.Rd
man/indexed_edges_to_graph.Rd
man/interval_index.Rd
man/is_dhist.Rd
man/is_numeric_vector_1d.Rd
man/make_named_ego_graph.Rd
man/mean_centre_dhist.Rd
man/mean_density_binned_graphlet_counts.Rd
man/min_emd.Rd
man/min_emd_exhaustive.Rd
man/min_emd_optimise.Rd
man/min_emd_optimise_fast.Rd
man/netdis.Rd
man/netdis.plot.Rd
man/netdis_centred_graphlet_counts.Rd
man/netdis_const_expected_counts.Rd
man/netdis_expected_counts.Rd
man/netdis_expected_counts_ego.Rd
man/netdis_many_to_many.Rd
man/netdis_one_to_many.Rd
man/netdis_one_to_one.Rd
man/netdis_subtract_exp_counts.Rd
man/netdis_uptok.Rd
man/netemd.plot.Rd
man/netemd_many_to_many.Rd
man/netemd_one_to_one.Rd
man/netemd_single_pair.Rd
man/normalise_dhist_mass.Rd
man/normalise_dhist_variance.Rd
man/orbit_key.Rd
man/orbit_to_graphlet_counts.Rd
man/read_simple_graph.Rd
man/read_simple_graphs.Rd
man/scale_graphlet_count.Rd
man/scale_graphlet_counts_ego.Rd
man/shift_dhist.Rd
man/shift_to_next_alignment.Rd
man/simplify_graph.Rd
man/single_density_bin.Rd
man/sort_dhist.Rd
man/virusppi.Rd
man/worldtradesub.Rd
man/zeros_to_ones.Rd
network_comparison.Rproj
src/.gitignore
src/Makevars
src/RcppExports.cpp
src/counts_from_observations.cpp
src/emd_fast_no_smoothing.cpp
src/emd_fast_no_smoothing.h
src/test-runner.cpp
src/test_emd_fast_no_smoothing.cpp
tests/testthat.R
tests/testthat/test-cpp.R
tests/testthat/test_dhist.R
tests/testthat/test_emd.R
tests/testthat/test_graph_binning.R
tests/testthat/test_measures_net_dis.R
tests/testthat/test_measures_net_emd.R
tests/testthat/test_orca_interface.R
tests/testthat/test_utility_functions.R
vignettes/.gitignore
vignettes/ManyToMany.Rmd
vignettes/NetEmdTimeOrdering.Rmd
vignettes/NetEmdTimeOrdering_cache/html/__packages
vignettes/NetEmdTimeOrdering_cache/html/unnamed-chunk-3_fa1cab3be9f1ecfbe870c0476447ff7d.RData
vignettes/NetEmdTimeOrdering_cache/html/unnamed-chunk-3_fa1cab3be9f1ecfbe870c0476447ff7d.rdb
vignettes/NetEmdTimeOrdering_cache/html/unnamed-chunk-3_fa1cab3be9f1ecfbe870c0476447ff7d.rdx
vignettes/NetEmdTimeOrdering_files/figure-html/unnamed-chunk-2-1.png
vignettes/NetEmdTimeOrdering_files/figure-html/unnamed-chunk-6-1.png
vignettes/NetdisGPStepByStep.Rmd
vignettes/NetdisStepByStep.Rmd
vignettes/NewNetdisCustomisations.Rmd
vignettes/PreComputedProps.Rmd
vignettes/V-Menu.Rmd
vignettes/default_pairwise_usage.Rmd
vignettes/dendrogram_example_net_dis.Rmd
vignettes/dendrogram_example_net_emd.Rmd
vignettes/netdis_customisations.Rmd
vignettes/netdis_pairwise_comparisons.Rmd
vignettes/quickstart_netdis_2graphs.Rmd
