Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

v1.4.0 #295

Merged
merged 97 commits into from
Jul 19, 2024
Merged

v1.4.0 #295

merged 97 commits into from
Jul 19, 2024

Commits on Mar 28, 2024

  1. Fixed node_constraint() to work with weighted twomode networks, thank… 

    …s to Toshitaka Izumi for spotting this
    @jhollway
    jhollway committed Mar 28, 2024
    Configuration menu
    Copy the full SHA
    f9f3134 View commit details
    Browse the repository at this point in the history

Commits on Apr 30, 2024

  1. Updated migraph logo with stocnet address, colorsafe colorway, and la… 

    …rger nodes and ties
    @jhollway
    jhollway committed Apr 30, 2024
    Configuration menu
    Copy the full SHA
    71c0f19 View commit details
    Browse the repository at this point in the history

Commits on May 2, 2024

  1. Added network_independence() for calculating the number of nodes in t… 

    …he largest independent set
    @jhollway
    jhollway committed May 2, 2024
    Configuration menu
    Copy the full SHA
    7354c57 View commit details
    Browse the repository at this point in the history

Commits on May 20, 2024

  1. Added .corDiag() and .corRecip() for calculating nodal correlations w… 

    …ithout the diagonal and including reciprocated ties
    @jhollway
    jhollway committed May 20, 2024
    Configuration menu
    Copy the full SHA
    77a94a7 View commit details
    Browse the repository at this point in the history

Commits on May 22, 2024

  1. equivalence functions can now be used in e.g. mutate() without specif… 

    …ying .data
    @jhollway
    jhollway committed May 22, 2024
    Configuration menu
    Copy the full SHA
    8b320f8 View commit details
    Browse the repository at this point in the history

  2. Fixed bug in node_tie_census() where census only conducted on second … 

    …mode of two-mode networks
    @jhollway
    jhollway committed May 22, 2024
    Configuration menu
    Copy the full SHA
    77d3ace View commit details
    Browse the repository at this point in the history

  3. Added thisRequires() helper into migraph (copy from manynet)

    @jhollway
    jhollway committed May 22, 2024
    Configuration menu
    Copy the full SHA
    5721384 View commit details
    Browse the repository at this point in the history

  4. Using thisRequires() for ggdendro dependency

    @jhollway
    jhollway committed May 22, 2024
    Configuration menu
    Copy the full SHA
    78102ca View commit details
    Browse the repository at this point in the history

  5. Added .corComplex()

    @jhollway
    jhollway committed May 22, 2024
    Configuration menu
    Copy the full SHA
    06a3c2e View commit details
    Browse the repository at this point in the history

  6. Added to_correlation()

    @jhollway
    jhollway committed May 22, 2024
    Configuration menu
    Copy the full SHA
    dc264a1 View commit details
    Browse the repository at this point in the history

  7. make_node_member() now converts numeric results to LETTER character r… 

    …esults
    @jhollway
    jhollway committed May 22, 2024
    Configuration menu
    Copy the full SHA
    3071def View commit details
    Browse the repository at this point in the history

  8. Fixed how cluster_concor handles unlabelled networks

    @jhollway
    jhollway committed May 22, 2024
    Configuration menu
    Copy the full SHA
    ab2e886 View commit details
    Browse the repository at this point in the history

  9. cluster_hierarchical() and cluster_concor() now use to_correlation() … 

    …instead of stats::cor()
    @jhollway
    jhollway committed May 22, 2024
    Configuration menu
    Copy the full SHA
    88136a2 View commit details
    Browse the repository at this point in the history

  10. Fixed how cluster_concor() handles two-mode networks

    @jhollway
    jhollway committed May 22, 2024
    Configuration menu
    Copy the full SHA
    560b61d View commit details
    Browse the repository at this point in the history

  11. Fixed bug where cluster_concor() cutoff resulted in unsplit groups

    @jhollway
    jhollway committed May 22, 2024
    Configuration menu
    Copy the full SHA
    48db250 View commit details
    Browse the repository at this point in the history

Commits on May 23, 2024

  1. node_tie_census() now works on longitudinal network data

    @jhollway
    jhollway committed May 23, 2024
    Configuration menu
    Copy the full SHA
    f9f08d9 View commit details
    Browse the repository at this point in the history

  2. print.node_member() now works with categorical membership vectors, de… 

    …clares how many groups before reporting the vectors
    @jhollway
    jhollway committed May 23, 2024
    Configuration menu
    Copy the full SHA
    9460c7c View commit details
    Browse the repository at this point in the history

  3. All measures and membership functions now infer network data where no… 

    …t present
    @jhollway
    jhollway committed May 23, 2024
    Configuration menu
    Copy the full SHA
    0c760bb View commit details
    Browse the repository at this point in the history

  4. Added argument to overwrite default behaviour in to_correlation()

    @jhollway
    jhollway committed May 23, 2024
    Configuration menu
    Copy the full SHA
    a878a56 View commit details
    Browse the repository at this point in the history

  5. Fixed node_member tests

    @jhollway
    jhollway committed May 23, 2024
    Configuration menu
    Copy the full SHA
    bb91b88 View commit details
    Browse the repository at this point in the history

  6. Added tests for to_correlation()

    @jhollway
    jhollway committed May 23, 2024
    Configuration menu
    Copy the full SHA
    d153c72 View commit details
    Browse the repository at this point in the history

  7. Fixed bug where print.node_motif() wasn't printing the requested numb… 

    …er of lines
    @jhollway
    jhollway committed May 23, 2024
    Configuration menu
    Copy the full SHA
    ad67d14 View commit details
    Browse the repository at this point in the history

  8. Fixed remaining documentation bugs

    @jhollway
    jhollway committed May 23, 2024
    Configuration menu
    Copy the full SHA
    6eb9ec7 View commit details
    Browse the repository at this point in the history

  9. Developed migraph README further

    @jhollway
    jhollway committed May 23, 2024
    Configuration menu
    Copy the full SHA
    d459976 View commit details
    Browse the repository at this point in the history

  10. #minor bump and NEWS

    @jhollway
    jhollway committed May 23, 2024
    Configuration menu
    Copy the full SHA
    c3626f8 View commit details
    Browse the repository at this point in the history

Commits on May 24, 2024

  1. Fixed small issue with cluster_concor()

    @henriquesposito
    henriquesposito committed May 24, 2024
    Configuration menu
    Copy the full SHA
    f875229 View commit details
    Browse the repository at this point in the history

  2. Revert "Fixed small issue with cluster_concor()" 

    This reverts commit f875229.
    @jhollway
    jhollway committed May 24, 2024
    Configuration menu
    Copy the full SHA
    b39012b View commit details
    Browse the repository at this point in the history

  3. Updated migraph version number in NEWS

    @jhollway
    jhollway committed May 24, 2024
    Configuration menu
    Copy the full SHA
    f30fa52 View commit details
    Browse the repository at this point in the history

  4. Avoid i undefined issue

    @jhollway
    jhollway committed May 24, 2024
    Configuration menu
    Copy the full SHA
    3aff8fc View commit details
    Browse the repository at this point in the history

  5. Try again

    @jhollway
    jhollway committed May 24, 2024
    Configuration menu
    Copy the full SHA
    3f47ac1 View commit details
    Browse the repository at this point in the history

Commits on Jun 13, 2024

  1. Added descriptions to tutorials

    @jhollway
    jhollway committed Jun 13, 2024
    Configuration menu
    Copy the full SHA
    def74ee View commit details
    Browse the repository at this point in the history

Commits on Jun 14, 2024

  1. Hierarchical clustering algorithms now return dendrograms

    @jhollway
    jhollway committed Jun 14, 2024
    Configuration menu
    Copy the full SHA
    4d15f50 View commit details
    Browse the repository at this point in the history

  2. node_roulette() renamed to node_in_roulette()

    @jhollway
    jhollway committed Jun 14, 2024
    Configuration menu
    Copy the full SHA
    8bfed72 View commit details
    Browse the repository at this point in the history

  3. node_components() renamed node_in_component() NB no longer plural!, n… 

    …ode_weak_components() now node_in_weak(), node_strong_components() now node_in_strong()
    @jhollway
    jhollway committed Jun 14, 2024
    Configuration menu
    Copy the full SHA
    3d8e1cb View commit details
    Browse the repository at this point in the history

  4. Moved to_correlation() to manynet, filled in _in_ defunct

    @jhollway
    jhollway committed Jun 14, 2024
    Configuration menu
    Copy the full SHA
    a3c369c View commit details
    Browse the repository at this point in the history

  5. node_core() renamed to node_in_core(), node_coreness() now returns no… 

    …de_measure output
    @jhollway
    jhollway committed Jun 14, 2024
    Configuration menu
    Copy the full SHA
    42d2d5c View commit details
    Browse the repository at this point in the history

  6. node_equivalence(), node_structural_equivalence(), node_regular_equiv… 

    …alence() and node_automorphic_equivalence() renamed to node_in_equivalence(), node_in_structural(), node_in_regular(), and node_in_automorphic()
    @jhollway
    jhollway committed Jun 14, 2024
    Configuration menu
    Copy the full SHA
    52b24f4 View commit details
    Browse the repository at this point in the history

  7. node_edge_betweenness(), node_fast_greedy(), node_leading_eigen(), an… 

    …d node_walktrap() renamed to node_in_betweenness(), node_in_greedy(), node_in_eigen(), and node_in_walktrap(), and all now retain hierarchical information so that the dendrograms can be plotted
    @jhollway
    jhollway committed Jun 14, 2024
    Configuration menu
    Copy the full SHA
    45e7470 View commit details
    Browse the repository at this point in the history

  8. node_fluid(), node_infomap(), node_kernaghinlin(), node_leiden(), nod… 

    …e_louvain(), node_optimal(), and node_spinglass() renamed to node_in_fluid(), node_in_infomap(), node_kernaghinlin(), node_in_leiden(), node_in_louvain(), node_in_optimal(), and node_in_spinglass()
    @jhollway
    jhollway committed Jun 14, 2024
    Configuration menu
    Copy the full SHA
    3f9f3fa View commit details
    Browse the repository at this point in the history

Commits on Jun 16, 2024

  1. Added parallelisation to testthat tests

    @jhollway
    jhollway committed Jun 16, 2024
    Configuration menu
    Copy the full SHA
    dffdb59 View commit details
    Browse the repository at this point in the history

  2. node_exposure() now sums tie weights where passed a weighted network

    @jhollway
    jhollway committed Jun 16, 2024
    Configuration menu
    Copy the full SHA
    9524ff7 View commit details
    Browse the repository at this point in the history

Commits on Jun 17, 2024

  1. node_kernaghinlin() renamed to node_in_partition()

    @jhollway
    jhollway committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    c5f9315 View commit details
    Browse the repository at this point in the history

  2. Fixed _in_ documentation

    @jhollway
    jhollway committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    ffa25c5 View commit details
    Browse the repository at this point in the history

  3. Fixed precisions in testthat tests related to reliance on newer version

    @jhollway
    jhollway committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    1f456a0 View commit details
    Browse the repository at this point in the history

  4. Fixed community documentation

    @jhollway
    jhollway committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    12a8226 View commit details
    Browse the repository at this point in the history

  5. Fixed cluster to_correlation dependence

    @jhollway
    jhollway committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    654c294 View commit details
    Browse the repository at this point in the history

  6. Renamed test_gof() to test_fit() to improve readability, split test d… 

    …ocumentation
    @jhollway
    jhollway committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    cc6dc72 View commit details
    Browse the repository at this point in the history

  7. Added test_distribution() to test whether two vectors/distributions a… 

    …re from the same distribution
    @jhollway
    jhollway committed Jun 17, 2024
    Configuration menu
    Copy the full SHA
    506ec64 View commit details
    Browse the repository at this point in the history

Commits on Jun 18, 2024

  1. Updated function names in tutorials

    @jaeltan
    jaeltan committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    3833dd7 View commit details
    Browse the repository at this point in the history

  2. Updated equivalence function names in function description

    @jaeltan
    jaeltan committed Jun 18, 2024
    Configuration menu
    Copy the full SHA
    43eb71b View commit details
    Browse the repository at this point in the history

Commits on Jun 23, 2024

  1. Migrated cluster and k to manynet

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    5e06e2b View commit details
    Browse the repository at this point in the history

  2. Migrated centrality measures to manynet

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    22c4b43 View commit details
    Browse the repository at this point in the history

  3. Migrated node_roulette() to manynet

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    bef956a View commit details
    Browse the repository at this point in the history

  4. Migrated closure measures to manynet

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    dc84ea5 View commit details
    Browse the repository at this point in the history

  5. Migrated components to manynet

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    d06531b View commit details
    Browse the repository at this point in the history

  6. Migrated equivalence memberships to manynet

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    04edafc View commit details
    Browse the repository at this point in the history

  7. Migrated cohesion measures to manynet

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    1cdc41e View commit details
    Browse the repository at this point in the history

  8. Migrated community memberships to manynet

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    9b4873b View commit details
    Browse the repository at this point in the history

  9. Migrated core to manynet

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    f783c65 View commit details
    Browse the repository at this point in the history

  10. Migrated heterogeneity measures to manynet

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    b1d6578 View commit details
    Browse the repository at this point in the history

  11. Migrated hierarchy measures to manynet

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    56f8ae3 View commit details
    Browse the repository at this point in the history

  12. Migrated diffusion measures to manynet

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    08369d7 View commit details
    Browse the repository at this point in the history

  13. Migrated over_ to manynet

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    7297417 View commit details
    Browse the repository at this point in the history

  14. Migrated holes measures to manynet

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    e756c77 View commit details
    Browse the repository at this point in the history

  15. Migrated feature measures to manynet

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    cf23995 View commit details
    Browse the repository at this point in the history

  16. Migrated census/motifs to manynet

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    80b2d74 View commit details
    Browse the repository at this point in the history

  17. Migrated residual classes to manynet

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    6fb85db View commit details
    Browse the repository at this point in the history

  18. Migrated community tutorial to manynet

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    607c7ec View commit details
    Browse the repository at this point in the history

  19. Migrated position tutorial to manynet

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    68c7fbd View commit details
    Browse the repository at this point in the history

  20. Migrated topology tutorial to manynet

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    c5a9918 View commit details
    Browse the repository at this point in the history

  21. Migrated defunct warnings to manynet

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    b7eef6e View commit details
    Browse the repository at this point in the history

  22. test_fit() no longer measures fit against steps where there is no cov… 

    …ariance
    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    3af95db View commit details
    Browse the repository at this point in the history

  23. Migrated tests to manynet

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    e72e10c View commit details
    Browse the repository at this point in the history

  24. Dropped old defuncts

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    5ece8c6 View commit details
    Browse the repository at this point in the history

  25. Fixed documentation bug in regression

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    779dd2a View commit details
    Browse the repository at this point in the history

  26. Fixed missing scale_y_discrete reexport

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    1daea5a View commit details
    Browse the repository at this point in the history

  27. Corrected manynet dependencies and net_ naming in tests

    @jhollway
    jhollway committed Jun 23, 2024
    Configuration menu
    Copy the full SHA
    8137de6 View commit details
    Browse the repository at this point in the history

Commits on Jul 3, 2024

  1. Fixed bug in test_random() where parameters were passed to manynet::g… 

    …enerate_random() instead of the original object, which is processed more intuitively within manynet::generate_random() (thanks @RWKrause)
    @jhollway
    jhollway committed Jul 3, 2024
    Configuration menu
    Copy the full SHA
    9c1745f View commit details
    Browse the repository at this point in the history

  2. Corrected that test_random() returns results on edge-conditioned unif… 

    …orm graphs, not size
    @jhollway
    jhollway committed Jul 3, 2024
    Configuration menu
    Copy the full SHA
    0749b5d View commit details
    Browse the repository at this point in the history

Commits on Jul 8, 2024

  1. Declared global variables

    @jhollway
    jhollway committed Jul 8, 2024
    Configuration menu
    Copy the full SHA
    15c8a7c View commit details
    Browse the repository at this point in the history

  2. Fixed various dependency issues

    @jhollway
    jhollway committed Jul 8, 2024
    Configuration menu
    Copy the full SHA
    cfd8f34 View commit details
    Browse the repository at this point in the history

Commits on Jul 9, 2024

  1. Explaining situation in cran-comments

    @jhollway
    jhollway committed Jul 9, 2024
    Configuration menu
    Copy the full SHA
    fba418b View commit details
    Browse the repository at this point in the history

  2. Commenting out tests/examples for now

    @jhollway
    jhollway committed Jul 9, 2024
    Configuration menu
    Copy the full SHA
    63dcb14 View commit details
    Browse the repository at this point in the history

Commits on Jul 18, 2024

  1. specificationAdvice now ignores absent ego terms for undirected networks

    @jhollway
    jhollway committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    fcb93b7 View commit details
    Browse the repository at this point in the history

  2. Dropped centrality tutorial (in manynet)

    @jhollway
    jhollway committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    fa38ea2 View commit details
    Browse the repository at this point in the history

  3. Renamed regression tutorial the diversity tutorial

    @jhollway
    jhollway committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    a94ca76 View commit details
    Browse the repository at this point in the history

  4. Initial section of diversity tutorial now about visualisation

    @jhollway
    jhollway committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    c305c0f View commit details
    Browse the repository at this point in the history

  5. Added richness section

    @jhollway
    jhollway committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    fff75c2 View commit details
    Browse the repository at this point in the history

  6. Diversity section now split from heterophily section to make passage … 

    …through the tutorial more straightforward
    @jhollway
    jhollway committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    d1cdef4 View commit details
    Browse the repository at this point in the history

  7. Updated CUG test section

    @jhollway
    jhollway committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    2931c54 View commit details
    Browse the repository at this point in the history

  8. Updated QAP test section

    @jhollway
    jhollway committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    7251a42 View commit details
    Browse the repository at this point in the history

  9. Updated network regression section of diversity tutorial, making sure… 

    … that it includes best practice in terms of specification
    @jhollway
    jhollway committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    e26c403 View commit details
    Browse the repository at this point in the history

  10. Reinstated test tests

    @jhollway
    jhollway committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    d7e0e15 View commit details
    Browse the repository at this point in the history

  11. Updated pkgdown and favicons

    @jhollway
    jhollway committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    3679d3d View commit details
    Browse the repository at this point in the history

  12. #minor bump and updated description to match package trim

    @jhollway
    jhollway committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    e4caeb6 View commit details
    Browse the repository at this point in the history

  13. Updated README to match package trim, added alt text

    @jhollway
    jhollway committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    d5e8d7e View commit details
    Browse the repository at this point in the history

  14. Using html instead of markdown for images so alt text doesn't appear … 

    …as title
    @jhollway
    jhollway committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    a729dd6 View commit details
    Browse the repository at this point in the history