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fastSmoothEMD code review suggestions #129
Commits on May 2, 2019
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Commits on Jun 7, 2019
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Commits on Jul 23, 2019
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2 graph vignette and fn changes in progress
Moving towards: * A netdis function that takes two input graphs and a reference graph. * Sub-functions that follow through paper steps, sequentially applied with output of one providing input for next.
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Commits on Jul 24, 2019
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dropping of small ego networks moved to make_named_ego_graph
Code to filter ego networks with fewer than threshold nodes/edges was duplicated many places. Added that functionality to make_named_ego_graph, where ego networks originally generated. Also, remove unnecessary duplication of simplifying in read_simple_graphs function, as it's already performed in read_simple_graph (which read_simple_graphs calls).
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Commits on Jul 25, 2019
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min_ego_nodes and min_ego_edges added to test_orca_interface
Default behaviour of ego network generating functions is now min_ego_nodes <- 3 and min_ego_edges <- 1. Set these to zero in function calls so orca tests now passing. Should implement tests to check that filtering of small ego networks is working as expected (i.e. when min_ego_edges and min_ego_nodes > 0)
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ego filtering args added to test_measures_net_dist
ego network generating functions now take min_ego_edges and min_ego_nodes arguments to filter out small ego networks, which default to 1 and 3 respectively. Set to zero for tests. Filtering is probably happening explicitly elsewhere in the tests - could be removed with min_ego_edges and min_ego_nodes given non-zero values as appropriate.
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Commits on Jul 26, 2019
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Commits on Jul 29, 2019
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working 2 graph vignette for netdis
Vignette to calculate netdis for 2 query graphs and a reference network: * Follows steps of paper. * Output of previous step used as input to next step (as much as possible). * Calculates netdis for all graphlet sizes up to max_graphlet_size * No explicit calls to purrr - all hidden in functions for each step. * Needs a lot of tidying of function names, docs, removal of potentially obsolete functions etc. Questions: * What should be in top level netdis function - current netdis function takes centred graphlet counts (i.e. output of all but last step). Should that be parent function taking two query graphs, ref graph, and parameters? * How to implement comparison of many graphs? This may differ depending on choice above - e.g. when comparing many graphs ideally don't want to be re-calculating ego nets and graphlet counts each time.
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Commits on Jul 30, 2019
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Commits on Aug 30, 2019
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started constant counts vignette
but bugs - netdis_expected_graphlet_counts applies scaling so shouldn't be used for GP approx or constant count subtraction as written
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Commits on Sep 2, 2019
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Commits on Sep 4, 2019
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Commits on Sep 5, 2019
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Commits on Sep 6, 2019
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Commits on Sep 11, 2019
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Commits on Sep 23, 2019
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Commits on Sep 25, 2019
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Commits on Sep 26, 2019
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Commits on Sep 27, 2019
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Commits on Oct 8, 2019
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stopped passing around ego networks
+ started to implement possibility to pass in graphlet counts and a constant expected counts value
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Commits on Oct 10, 2019
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Commits on Oct 15, 2019
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Commits on Oct 17, 2019
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Commits on Oct 18, 2019
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Commits on Nov 7, 2019
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Commits on Nov 8, 2019
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Commits on Nov 12, 2019
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Fix for NA exp counts in geometric poisson
And added test for geometric poisson
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Commits on Mar 10, 2020
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Commits on Mar 12, 2020
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Commits on Apr 17, 2020
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Commits on Apr 20, 2020
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Commits on Apr 21, 2020
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Merge branch 'fastSmoothEMD-review' of https://github.com/alan-turing…
…-institute/network-comparison into fastSmoothEMD-review
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Merge pull request #122 from alan-turing-institute/118-netdis-interfa…
…ce-refactor Refactoring of Netdis code and linting of whole package (including NetEMD). - Luis has reviewed the code and approved it being merged. - Andrew is also ok for NetEMD linting changes to be merged.
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Commits on Apr 22, 2020
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Commits on Apr 23, 2020
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Commits on Jun 8, 2020
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Commits on Jun 11, 2020
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Creation of a small menu of vignettes for the package.
Creation of a the simple case usage of the different network comparison methods with their default settings.
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Commits on Jun 12, 2020
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Change to names of dhist1 to dhist_1. Modification and renaming of ne…
…t_emd function to net_emd_one_to_one. It now accepts graph objects too.
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Additional automatic changes to files after check and clean+rebuild (…
…this changes should not be relevant as they are mostly formatting of the code)
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Commits on Jun 13, 2020
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Rename and modifications to net_emd to net_emd_one_to_one - test are …
…consequently modified in order to let the package pass the checks.
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Commits on Jun 15, 2020
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Changes to net_emd_one_to_one so that it takes graphs, matrices and d…
…hist objects. Added some examples on the function documentation and in the vignette default_pairwse_usage
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Commits on Jun 22, 2020
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Commits on Jun 23, 2020
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Modifications to introductory vignette, function name changes and add…
…ition of parameters, corresponding modifications to tests, added documentation of functions along with examples. Vignette default_pairwise_usage is now as a first completed draft.
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Latest package source built that is in use for pairwise comparisons c…
…alling networks or precomputed counts.
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Commits on Jun 24, 2020
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Important changes to functions for netdis_gp, mostly for the handling…
… of zero variance and divisions by zero.
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Commits on Jul 8, 2020
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Merge commit '11c6507ef676ab3cf3cb4bd69f775bbf81e91ff8' into Vignette…
…sAndDoc * commit '11c6507ef676ab3cf3cb4bd69f775bbf81e91ff8': bug fix missing graphlet_counts_ref add graphlet_counts_ref argument to netdis_one_to_many check for null graphlet_counts_ref as well as ref_graph make geometric poisson default if ref_graph null
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Commits on Jul 13, 2020
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Correct default functionallit of netdis call for GP variant. Renaming…
… of netemd_many_to_many that is currently causing some sort of issue, and changes to vignette of many to many comparisons.
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Commits on Jul 14, 2020
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Error on Netdis GP for graphs with a number of connected nodes smalle…
…r than 5 (default binning requirement of the number of egos per bin). Error obtained before: Error: node stack overflow Error during wrapup: node stack overflow This was caused by binning_fn in the call: binned_densities <- binning_fn(densities) The function binned_densities_adaptive has been modified to account for this possibility.
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Small update to function definition. There is a need to do a larger u…
…pdate for all functions in the vignettes.
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Commits on Dec 12, 2020
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Commits on Dec 14, 2020
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Small text edits and updates to multiple files in relation to Vignett…
…e 3 (many-to-many)
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Commits on Feb 3, 2021
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New data to be used in one of the vignettes. The dataset are world tr…
…ade networks from the NetEmd paper.
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Commits on Feb 4, 2021
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These files come from the cache in world trade vignette... perhaps th…
…is should be taken out
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Commits on Feb 8, 2021
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Merge pull request #135 from alan-turing-institute/VignettesAndDoc
Vignettes and doc
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Merge pull request #139 from alan-turing-institute/fix/132-purr-contains
replace purrr::contains with purrr::has_element
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Merge pull request #142 from alan-turing-institute/test-travis
Fix CI (/migrate to GitHub actions)
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Merge pull request #145 from alan-turing-institute/pkgdown
pkgdown (docs website)
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Merge branch 'fastSmoothEMD-review' of github.com:alan-turing-institu…
…te/network-comparison into fastSmoothEMD-review
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