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This release fixes a number of bugs found in a code review. Some
fixes change results, notably dyad_census_attr(),
triad_census_attr() (030C orientations),
graph_cor() (diagonal now excluded by default) and
sample_lfr() (now uses R’s random number generator).
dyad_census_attr() fixed: asymmetric dyads were dropped
when a group pair had edges in one direction only, and within-group
asymmetric dyads were always reported as 0. Named vertices returned all
zeros and graphs without edges errored. Within-group rows now report the
total asymmetric count in asym_ab and NA in
asym_ba. Multiple edges and loops are ignored.dyad_census_attr() and triad_census_attr()
now validate that the vertex attribute holds positive integers without
missing values.triad_census_attr() rewritten: it now runs in roughly
O(m * max degree) instead of O(n^3), e.g. seconds instead of hours for
thousands of nodes.triad_census_attr() fixed: the two orientations of
cyclic triads (030C) with three distinct attributes were merged into
T030C-abc; T030C-cba is now counted correctly.
With more than nine attribute values, names are separated by dots
(T030C-1.2.10) to avoid ambiguous labels. Multiple edges
and loops are ignored.str.igraph() no longer fails for graphs with a single
edge and only appends “…” to truncated attributes.bipartite_from_data_frame() now handles numeric and
factor columns (they were used as vertex ids or factor codes), and
merging multiple edges no longer fails with non-numeric edge
attributes.structural_equivalence() now works with multiple edges
and no longer needs memory quadratic in the number of vertices.sample_coreseq() now rejects impossible coreness
sequences (a k-core needs at least k + 1 nodes) and invalid input.graph_cartesian() and graph_direct() keep
vertex pairs without edges, and are vectorized.as_adj_list1() now returns all neighbors of directed
graphs, as documented (it returned only out-neighbors).graph_cor() now excludes the diagonal by default, the
standard definition of graph correlation. Use diag = TRUE
for the previous behavior. For igraph objects, the new attr
argument selects an edge attribute as weights.graph_kpartite() now uses
igraph::make_full_multipartite(), errors if the partition
sizes do not sum to n and stores the partition in the
vertex attribute type. The documentation now correctly says
it creates a complete k-partite graph.graph_from_multi_edgelist() stores the
weight column as edge attribute weight, so the
graphs are weighted, and validates it.split_graph() validates core.as_adj_weighted(), as_multi_adj(),
graph_cor() and core_periphery() work with the
upcoming igraph 3.0.0 and keep using unweighted adjacency matrices
unless an edge attribute is given.fast_cliques().sample_pa_homophilic() is faster, validates its input
and has working examples; results for a given seed are unchanged.core_periphery(method = "SA") now actually runs the GA
method as announced in its deprecation warning (it returned nothing
before).sample_lfr() now uses R’s random number generator, so
results are reproducible with set.seed() (before,
set.seed() had no effect).sample_lfr() with overlapping nodes
(on > 0) now works (it errored before):
V(g)$membership holds the first community of each vertex
and the new list attribute V(g)$memberships holds all
communities of each vertex.sample_lfr() now reports invalid parameter combinations
detected by the generator as informative R errors instead of “negative
length vectors are not allowed”, validates on,
om, min_community and
max_community, and is silent unless the new
verbose = TRUE is set. It warns if the degree sequence had
to be changed.sample_lfr() can be interrupted and no longer risks
endless loops when rewiring links. Unused C++ code of the LFR generator
was removed.str.igraphsample_lfr() in C++ (#9)str.igraph from working
(#10)reciprocity_cor()sample_lfr() (#9)added sample_pa_homophilic()
netUtilsbipartite_from_data_frame()graph_from_multi_edgelist() and
as_multi_adj()structural_equivalence()core_periphery()sample_coreseq()graph_cartesian() and
graph_direct()fast_cliques()as_adj_list1() and
as_adj_weighted()clique_vertex_mat()These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.