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Changelog

Source: NEWS.md

netrankr 2.0.0

This release fixes a large number of bugs found in a full code review. Several of them change numerical results for code that ran without errors before, hence the major version.

Breaking changes

These change results without an error. Please re-check analyses that use them.

  • indirect_relations() ignores an edge attribute weight for all types except "weights" and warns when it does so. Previously "dist_sp", "dist_resist" and "dist_lf" used weights silently, while all other types ignored them (and with igraph >= 3.0 the adjacency-based types would have picked them up too, giving meaningless values for "depend_curflow"). For weighted shortest path distances use igraph::distances(g) directly, for the weighted adjacency matrix type = "weights".
  • indirect_relations(type = "depend_rspn") counted every edge twice and omitted the 1/2 net flow factor. Values are now 1/4 of the previous ones and, as documented, converge to "depend_curflow" for rspxparam -> 0. Rankings are unaffected. Multiply by 4 to obtain the old values.
  • The entries of indirect_relations(type = "depend_rsps") now match the documented definition (expected number of visits on absorbing randomized shortest paths). Their row sums, the RSP betweenness, and hence rankings are unchanged. The old entries were wrong and cannot be restored.
  • walks_uptok() includes the j = 0 (identity) term, as documented. Use FUN = function(x, ...) walks_uptok(x, ...) - 1 for the old behaviour.
  • majorization_gap(norm = TRUE) on disconnected graphs divides the sum of the gaps of all components by the total number of edges, so the value stays in [0, 1]. Previously the normalised gaps of the components were added up.
  • For partial rankings with structurally equivalent nodes, exact_rank_prob() and mcmc_rank_prob() compute the expected ranks exactly (equivalent nodes are tied at the highest rank of their class, as for linear orders). Previously a heuristic was used.
  • mcmc_rank_prob() was biased (rejected moves were not counted as samples), so its estimates change.

Other changes that may require changes to code:

  • All functions taking a partial ranking P share one input validation: non-square input and NA are errors, and a non-zero diagonal is set to 0 with a warning (previously crashes, NAs or silently wrong results).
  • indirect_relations() errors for relations that are only defined on connected graphs ("dist_resist", "depend_curflow", "dist_rwalk", "depend_exp", "depend_rsps", "depend_rspn", and "depend_netflow" with netflowmode = "frac") instead of failing in LAPACK or returning NaNs.
  • compare_ranks() and is_preserved() error on NA (compare_ranks() counted such pairs as ties).
  • neighborhood_inclusion() simplifies graphs with loops or multiple edges with a warning (these gave a wrong preorder).
  • hyperbolic_index() and spectral_gap() reject directed graphs.
  • Removed the unexported, deprecated plot_rank_intervals(). Use plot(rank_intervals(P)).
  • Requires R >= 3.5.0 and igraph >= 2.1.0.

Bug fixes

  • indirect_relations(type = "depend_sp") overflowed on graphs with many shortest paths.
  • positional_dominance(type = "two-mode") failed for matrices with column names and ignored benefit and map; with map = FALSE non-square one-mode input read out of bounds.
  • The random failure scenario of swan_combinatory() only removed k nodes (the number of repetitions) instead of all nodes, and failed for k > n.
  • majorization_gap() recycled vectors for disconnected graphs.
  • transitive_reduction() returned an empty matrix for reflexive input.
  • compare_ranks() overflowed for more than 65536 elements.
  • mcmc_rank_prob() evaluated the default rp after collapsing structurally equivalent nodes and silently did nothing for rp beyond the integer range.
  • indirect_relations(type = "depend_exp") ignored edges with multiplicity > 1.
  • hyperbolic_index() returned NaN for isolated nodes, spectral_gap() complex numbers for directed graphs.
  • index_builder(): fixed the generated code for "dist_walk" (used the log forest parameter) and without pipes (ignored the network name), the alpha sliders (duplicated input ids) and presets resetting the transformation.
  • aggregate_positions(type = "self") failed on Matrix objects.
  • Sparse (including pattern) and dense Matrix input failed in approx_rank_expected(), approx_rank_relative(), mcmc_rank_prob() and positional_dominance().
  • Plot methods did not restore par() on error and failed for a single index or more than 15 indices.

Improvements

Housekeeping

  • Tests use testthat 3rd edition; many new regression tests.
  • Replaced deprecated igraph calls; no use of the attr argument deprecated in igraph 3.0.
  • Native routines are registered; removed unused OpenMP flags.

netrankr 1.2.4

CRAN release: 2025-02-05

  • added functions from archived NetSwan package
  • removed deprecated igraph calls

netrankr 1.2.3

CRAN release: 2023-12-19

  • removed test causing issues on some platforms

netrankr 1.2.2

CRAN release: 2023-12-15

  • fixed goodpractice warnings #17
  • added more tests
  • added more documentation for index_builder #15
  • possibly breaking: removed mid point calculation from rank_intervals #12
  • upgraded igraph graph versions #23
  • printed some matrices in vignette indirect_relations #11

netrankr 1.2.1

CRAN release: 2023-08-20

  • fixed PKGNAME-package as per “Documenting packages” in R-exts.
  • fixed bibentry issue
  • fixed #21

netrankr 1.2.0

CRAN release: 2022-09-26

  • benchmark vignette is now reproducible with code and data from data-raw
  • internal changes after JOSS submission

netrankr 1.1.1

CRAN release: 2021-12-21

  • removed hcl.colors due to backward compatibility for R <3.6 (#9)

netrankr 1.1.0

CRAN release: 2021-09-03

  • neighborhood_inclusion() can return a sparse matrix (Matrix package now imported)
  • all functions support sparse matrices as inputs
  • added summary method for netrankr_full objects
  • added as.matrix method for netrankr_full objects to extract probability distributions
  • changed to on.exit(par(op)) in plot functions
  • all functions now through errors instead of warnings when the network is vertex transitive
  • better error handling if the input is not as expected
  • added legends to the default plot function for netrankr_full objects
  • added legend to the default plot function for netrankr_mcmc objects
  • changed default colors of the plot function for netrankr_interval objects to be more colorblind friendly

netrankr 1.0.0

CRAN release: 2021-07-16

  • added S3 class netrankr_full (result of exact_rank_prob()) with print and plot functions (#8)
  • added S3 class netrankr_interval (result of rank_intervals()) with print and plot functions (#8)
  • added S3 class netrankr_mcmc (result of mcmc_rank_prob()) with print and plot functions (#8)
  • added dbces11 graph (smallest graph with 5 different centers)
  • plot_rank_intervals() is now deprecated
  • ggplot2 no longer suggested

netrankr 0.3.0

CRAN release: 2020-09-09

netrankr 0.2.1

CRAN release: 2018-09-18

netrankr 0.2.0

CRAN release: 2018-01-08

  • added Rstudio addin to build more than 20 centrality indices
  • added indirect relations: dist_lf,dist_walk, depend_netflow, depend_exp, depend_rsps, depend_rspn, depend_curflow, dist_rwalk, dist_walk
  • API breaking: changed “dependencies” to “depend_sp” in indirect_relations()
  • API breaking: changed “geodesic” to “dist_sp” in indirect_relations()
  • API breaking: changed “resistance” to “dist_resist” in indirect_relations()
  • The above old types still work in this version
  • changed require to library in examples

netrankr 0.1.1

netrankr 0.1.0

  • first public release

netrankr 0.0.5

  • most function reimplemented in C++ for efficiency.
  • vignettes added: browseVignettes("netrankr")
  • added visualization function plot_rank_intervals()
  • spell checked and extended help

netrankr 0.0.1-0.0.4

initial builds, predominantely written in R.