sample parameter in sample_motifs() and ensure that the default sample.size is integer (#1568).all_simple_paths() documentation.cluster_optimal() does support directed graphs.See https://github.com/igraph/rigraph/blob/9828d7b11be330f994f07ae93a071b356eced903/src/vendor/cigraph/CHANGELOG.md for a complete changelog, in particular the section "Breaking changes".
p.value and p.precision arguments to fit_power_law() to control the computation of the p-value (#1546).as.undirected() signature thanks to @jhollway, regression introduced in igraph 2.1.0 (#1536).eigen_centrality(scale = ) (#1543).See https://github.com/igraph/rigraph/blob/05973441b83decdeab8cc9c500a642c00b924770/src/vendor/cigraph/CHANGELOG.md for a complete changelog, in particular the section "Breaking changes".
get.edge() and layout.grid.3d() which have been deprecated for 10 years (#1398).rlang::arg_match() in igraph.match.arg() (#1165).We are working towards a more consistent interface, especially as regards function naming: ultimately we want the igraph functions to use snake case. Please update your scripts and codebases as soon as you can.
independence_number() as an alias of ivs_size() (#1522).get_edge_ids() as an alias of get.edge.ids() (#1510).hub.score() and authority.score() both replaced by hits_scores() (#1352).erdos.renyi.game() and random.graph.game() (#1509).fit_power_law(implementation = "plfit.p") to compute the P-value (#1386).max_degree() (#1403).sample_chung_lu() (#1416).sample_degseq() and add the "edge.switching.simple" method (#1376).eccentricity() and radius() (#1211).add_shape() (#1478)..from() etc. with behavior similar to dplyr::across() (#1436): functions like .from() are meant to be used inside [ but now if an user misuses them, the error is more informative.graph.lattice() with its replacement make_lattice() (#1439).deprecated() as default value for circular argument to make_lattice() (#1431).subgraph_centrality() now ignores edge directions (#1414).disjoint_union() (#1375).PROTECT() (#1382).R_igraph_community_to_membership2() (#1367).sample_() (#1477).make_() manual page (#1476).is_separator() documentation based on C docs (#1467).?plot.common (@gvegayon) (#1413).sample_degseq() example (#1297).graph_from_adjacency_matrix() examples to avoid warnings (#1302).\dontrun{} with @examplesIf (#1307).sample_gnp() examples.betweenness() (#1489).centr_eigen_tmax() docs.edge_density() examples relevant.eigen_centrality() documentation.cluster_edge_betweenness() documentation.sample_forestfire() tests and example (#1318).CONTRIBUTING.md (#1423)..igraph.progress() and .igraph.status() more internal (#1516).See https://github.com/igraph/rigraph/blob/3299d31/src/vendor/cigraph/CHANGELOG.md for a complete changelog of the bundled C core, and https://github.com/igraph/rigraph/compare/f3fa58b..3299d31#diff-aeb78e0159780a9b26daabaf6f95f450b0cfec7161fc735f27ad69145a57dc84 for the changes since the igraph 2.0.1. (A permanent link to the most recent changelog of the C core used in the R package is https://github.com/igraph/rigraph/blob/main/src/vendor/cigraph/CHANGELOG.md.)
voronoi_cells() to compute the Voronoi partitioning of a graph (#1173).rglplot(edge_label = ) (#1267).x11() usage in example happen only in interactive sessions (#1301).min_st_separators() documentation (#1264).@seealso, and use it (#1270).@seealso from ?sample_pa (#1268).is_separator() and is_min_separator() (#1263).upgrade_graph() instead of the nonexisting upgrade_version() (#1252).is_bipartite() manual page from other manual page (#1230).CITATION.cff contains only the first three version components.barabasi.game() with sample_pa() (#1291).are_adjacent(), avoid deprecated igraph_are_connected() C function (#1254).See https://github.com/igraph/rigraph/blob/f3fa58b/src/vendor/cigraph/CHANGELOG.md for a complete changelog of the bundled C core, and https://github.com/igraph/rigraph/compare/1bd2bf79..f3fa58b#diff-aeb78e0159780a9b26daabaf6f95f450b0cfec7161fc735f27ad69145a57dc84 for the changes since the igraph 2.0.1. (A permanent link to the most recent changelog of the C core used in the R package is https://github.com/igraph/rigraph/blob/main/src/vendor/cigraph/CHANGELOG.md.)
g + vertices(1, 2, foo = 3) works again, regression introduced in igraph 2.0.0 (#1247).sample_pa() respects the out.seq and out.dist arguments again, regression introduced in igraph 2.0.0 (#1226).isomorphisms() and subgraph_isomorphisims(method = "vf2") work again, regression introduced in 2.0.0 (#1219).biconnected_components() now returns edge and vertex sequences again, regression introduced in 2.0.0 (#1213).order and order.out components returned by dfs(), regression introduced in 2.0.0 (#1179).realize_bipartite_degseq() creates a bipartite graph from two degree sequences (#1212).is_biconnected() checks if a graph is biconnected (#1204).distances() now supports the Floyd-Warshall algorithm (#1186).mean_distance() docs."dsatur" heuristic for greedy_vertex_coloring() (#1206).?articulation_points (#1191).isomorphisms() and subgraph_isomorphisms() (#1225).config.h defines HAVE___UINT128_T (#1216).which program during configuration (#1232).configure manage libxml multiple include paths (#1197).configure (#1235).HAVE_GFORTRAN flag for win and ucrt (#1171).make_empty_graph() is now fully auto-generated (#1068).is.R() which is deprecated in R 4.4.0.-Wlto warnings (#1163).This major release brings development in line with the C core at https://github.com/igraph/igraph. See https://github.com/igraph/rigraph/blob/1bd2bf79/src/vendor/cigraph/CHANGELOG.md for a complete changelog, in particular the section "Breaking changes". (A permanent link to the most recent changelog of the C core used in the R package is https://github.com/igraph/rigraph/blob/main/src/vendor/cigraph/CHANGELOG.md.)
Version 1.6.0 of the R package used version 0.9.9 of the C core. The changes in the 0.10 series of the C core are relevant for version 2.0.0 of the R package, but not all C core functions are exposed in the R interface. Changes to the implementation of some functions in the C core may be reflected in functions in the R package.
The change log below is a summary of the additional changes in the R interface.
get.edge.ids(multi = TRUE) and as_adjacency_matrix(edges = ) are no longer supported (#1101, #1080).
Remove NA padding for dfs(unreachable = FALSE)$order and $order.out and for bfs(unreachable = FALSE)$order, also for igraph_options(return.vs.es = FALSE) (#1062, #1124).
laplacian_matrix(normalized = TRUE) uses a different normalization method (#1102).
fit_power_law() no longer returns a KS.p component.
Remove default value for loops argument of centr_degree_tmax() (#1114).
as_adjacency_matrix() no longer supports attributes of type character (#1072).
Use lifecycle::deprecate_soft() for most deprecated functions (#1024, #1025, #1104).
The system libraries GLPK, GMP, and libxml2 are now mandatory for compiling from source.
Add scalar conversion checks in a few critical places (#1069).
Check that we receive a scalar when expecting a scalar in C code (#1051).
Check that matrix sizes are in the supported range before passing them to R (#1066).
transitivity() now produces a named vector in the local (weighted) case (#1057).
plot() correctly computes intersections between edges and rectangle vertices (#1021).
Fix compilation on Windows with spaces in the Rtools path (#1000).
Use 30 bits of R's RNG (#1079).
Breaking change: Remove NA padding for dfs(unreachable = FALSE)$order and $order.out and for bfs(unreachable = FALSE)$order, also for igraph_options(return.vs.es = FALSE) (#1062, #1124).
New k_shortest_paths() to compute the first k shortest paths between two vertices (#1028).
Add GitHub bug report form.
New vignette("deprecated-dot-case") that lists deprecated functions and their alternatives (#1013).
Move deprecation badge to top of doc pages.
Remove usage of get.adjacency() from intro vignettes (#1084).
Fix math formatting in fit_power_law() docs.
Fix incorrect usage in subgraph.edges() example.
Clarify that Infomap considers edge directions.
Improve edge connectivity docs (#1119).
Add some missing diacritics.
Use [] assignment for converting matrices (#1035).
Move towards autogenerating all bindings (#1043).
Use %||% from rlang (#1112).
Replace loop by lapply() when returning vertex and edge sets (#1033).
Do not duplicate prototypes, use a common header for rinterface.c and rinterface_extra.c (#1055).
Clean up some auto-generation code (#1031), remove unused parts from code generation (#1032), eliminate the use of some deprecated C functions.
Use integers for mode enum in cluster_label_prop().
Standardize the handling of some stimulus enum types (#1064).
Remove unused vectorlist / matrixlist destructors (#1070).
Remove unused stimulus type VERTEXSETLIST_INT (#1049).
Remove unused types (#1060).
Fix Stimulus definitions (#997).
Avoid deprecated R_igraph_automorphisms() (#999).
Use new ARPACK_DEFAULTS symbol from C core for default arpack options.
Ignore upstream CITATION file to avoid R CMD check NOTE (#1007).
Add Aviator configuration.
Add as_biadjacency_matrix() tests for named vectors (#1154, #1155).
Test transferring colors in isomorphism functions (#1050).
New arpack_defaults() replaces igraph.arpack.default and arpack_defaults lists (#800), with consistent usage checks (#966).
Define methods for ape::as.phylo() instead of own as_phylo() generic, remove deprecated asPhylo() (#763).
bfs() with unreachable nodes returns zero instead of NaN as rank (#956), and negative instead of NaN for dist (#926).
random_walk() adds one more step, the resulting list of vertices is of length steps + 1 (#934).
girth() returns Inf for acyclic graphs (#931).
Remove some behaviour / parameters that were deprecated in 1.3 (#842).
Remove scg_eps(), scg_group() and scg_semi_proj(), broken and no longer maintained (#946).
Fix printf() warning (#975).
Fix calls to isSymmetric() for matrix objects with a class (#965).
Reduce frequency of interruption checks (#957).
Change "incidence matrix" naming to "biadjacency matrix" (#962).
Add aliases using the neighborhood terminology for all ego functions: (#950).
Rename arguments to assortativity(values, values.in) from types1 and types2 (#952).
Add ellipsis to cluster_label_prop() (#954).
Placeholders for is_acyclic() and is_forest(), to be implemented in igraph 2.0.0 (#945).
is_tree(details = TRUE) designates the first vertex as root for non-trees (#935).
all_shortest_paths() returns the vertex list in both res and vpaths components (#930).
Improve symmetry check for adjacency matrices on input (#911).
Warn if non-symmetric undirected adjacency matrix (#904).
Remove duplicate \seealso{} (#948).
Update knnk() and sir() docs.
Fix formula in reciprocity() docs.
strength() does not give a warning when no weights are given.
Update sample_smallworld() manual page (#895).
Correct documentation for weighted cliques.
Update Erdos-Renyi model docs.
Clean up tests (#967).
Stabilize tests for cluster_label_prop() (#932), sample_pa() (#927), cluster_louvain() (#933), SIR (#936), sample_forestfire() (#929).
Hard-code graph used in test (#928).
Update GML test file (#925).
Improve test for sampling from Dirichlet distribution (#923).
Omit test that no longer holds with igraph 0.10 (#922).
Stabilize test in preparation for upgrade (#920).
Stabilize plot test (#919).
Fix checks.
estimate_betweenness(), estimate_edge_betweenness(), estimate_closeness() (#852).identical_graphs() now correctly detects identical graphs without node or edge attributes (#757).Change ownership rules of attribute objects (#870).
R_SEXP_to_igraph() and R_SEXP_to_igraph_copy() get igraph_t object from external pointer (#865).
Remove ETIME() call from Fortran code, already in CRAN version 1.5.0.1 (#858).
Ensure that _GNU_SOURCE is always defined (#877).
Fix make clean (#860).
Fix generation of code for functions with VERTEX_COLOR out-arguments (#850).
Use -lquadmath in Makevars.win, for compatibility with alternative R distributions such as Microsoft R Open (#855).
getRversion() uses strings.
Add cffr file and a GHA workflow that updates it automatically (#873).
Undeprecate neighborhood() (#851).
Remove redundant reference to AUTHORS from DESCRIPTION.
estimate_betweenness(), estimate_edge_betweenness(), estimate_closeness() (#852).The internal format of graph objects has changed in a mostly backward-compatible way, to prepare for upgrading the C core to 0.10. Details are described at https://github.com/igraph/rigraph/wiki/The-igraph-object-format. Accessing graph objects that have been created with an older igraph version give a clean error message with instructions (#832). The new format cannot be read by igraph 1.4.3 or older, the following error is raised when trying to do so:
This graph was created by an old(er) igraph version.
Call upgrade_graph() on it to use with the current igraph version
For now we convert it on the fly...
Error in is_directed(object) :
REAL() can only be applied to a 'numeric', not a 'NULL'
The only supported remedy is to upgrade the igraph package to version 1.5.0 or later.
graph_version() now returns an integer scalar (#832, #847), 4 as of igraph 1.5.0 (#835).
Vertex and edge sequences are converted to numeric vectors when used in attributes (#808).
New largest_component() returns the largest connected component (#786, @ngmaclaren).
make_graph() when simplify = ... is used with a non-formula (#834).Add more tests for graph_from_literal() (#826).
Reenable serialization test and tests for dyad_census(), stabilize tests (#809, #822, #823).
The documentation for the R package is now hosted at https://r.igraph.org/ (#780).
Update vignette("installation-troubleshooting").
Fix use of deprecated functions in examples, e.g., replace gsize() by ecount() (#827).
Fix typos in ?eigen_centrality docs (@JJ).
Add DOI to CITATION (#773).
Add data for old igraph versions as constructed objects, and tests (#838).
Ensure we're always using named indexes to access the internal data structure (#784).
Prepare migration to igraph/C 0.10 (#781).
Update generated interface (#765).
Remove igraph.eigen.default() and eigen_defaults, introduce internal eigen_defaults() as a function (#741).
Remove broken nexus*() functions (#705), and srand() (#701).
Update C core.
ARPACK-based calculations are now interruptible.
shortest_paths() and all_shortest_paths() no longer crash when an invalid from vertex is passed and weights are being used.
See diff for details.
Use true vertex names for printing vertex sets. If a vertex set captures a relationship between vertices (e.g., the father component of bfs()), the vertex set is printed as a named vector (#754).
Suggest restarting R session after fatal error (#745).
as_long_data_frame() now correctly processes vertex attributes and works with graphs without vertex attributes (#748).
as.hclust(hrg.fit(g)) works again (#721).
The documentation is now available at https://igraph.org/ (#743).
Reorganize function reference (#662).
Replace graph() with make_graph() in examples (#738).
Add docs for as.hclust.igraphHRG() (#733).
Merged man page of hub_score() and authority_score() (#698).
Refactor contributors listing (#647).
Improve "family" titles (#679).
Improve docs of ego/neighborhood functions.
Improve transitivity() docs.
Introduce cpp11 package to improve error handling in the long run (#720).
Avoid longjmp for error handling and interrupts (#751).
as.hclust.igraphHRG uses .Call() interface (#727).
console() now works again and provides a Tcl/Tk based UI where igraph can post status messages and progress info (#664).
Fix errors when printing long vertex names (#677, @ahmohamed).
Fix regression that broke builds on some systems (e.g., GCC version 5 or earlier), introduced in igraph 1.4.0 (#670, #671).
fit_hrg() does not crash any more when called with a graph that has less than three vertices.
Fix warning about yyget_leng() returning wrong type when using LTO (#676).
Don't mention C++11 or C++17 for best compatibility with both newest R and older compilers, while still requesting a C++ compiler for linking.
Don't ignore build/ when building the package because the vignette index is built there.
Skip plot test entirely on R-devel.
Avoid submodules for building igraph (#674).
Makevars cleanup (#671).
Add Zenodo configuration file.
tkplot() gained a palette argument and it is now using the same palette as plot() by default, for sake of consistency.plot.igraph() gained a loop.size argument that can be used to scale the common radius of the loop edges.cluster_leading_eigen().igraph_version() returned an invalid value in 1.3.4, this is now corrected.par(xpd=...) is now restored after plotting a graph.as.dendrogram.communities() for large dendrograms, thanks
to @pkharchenko (see PR #292).graph_from_incidence_matrix() that prevented the creation of directed graphs with mode="all" from dense or sparse matrices.dfs() accidentally returned zero-based root vertex indices in the result object; this is now fixed and the indices are now 1-based.as_graphnel() does not duplicate loop edges any more.as_graphnel() now checks that the input graph has no multi-edges. Multi-edges are not supported by the graphNEL class.convex_hull() now returns the vertices of the convex hull with 1-based indexing.rgl.*() function calls in the codebase were replaced with equivalent *3d() function calls in preparation for upcoming deprecations in rgl (see PR #619)plot.igraph() does not use the frame=... partial argument any more when calling plot.default(). The default NULL value of frame.plot is now also handled correctly.hub_score() and authority_score() considered self-loops only once on the diagonal of the adjacency matrix of undirected graphs, thus the result was not identical to that obtained by eigen_centrality() on loopy undirected graphs. This is now corrected.distances() no longer ignores the mode parameter when algorithm='johnson'.automorphisms() was renamed to count_automorphisms(); the old name is still available, but it is deprecated.main branch directly.pkgdown thanks to @maelle (see #645). This will eventually become the official homepage.Added:
mark.groups=... argument of plot.igraph() now accepts communities
objectsFixed:
Negative degree exponents are not allowed any more in sample_pa() and
sample_aging_pa().
Package updated to be compatible with Matrix 1.5.
Other:
Added:
sample_asym_pref() now returns the generated types of the vertices in the
vertex attributes named outtype and intype.Fixed:
layout_nicely() does not recurse infinitely any more if it is assigned to
the layout attribute of a graph
layout_nicely() now ignores edge weights when there are non-positive
edge weights. This is needed because igraph 1.3.3 started validating edge
weights in layout_with_fr() and layout_with_drl(), resulting in
errors when layout_nicely() was used on weighted graphs with negative
weights. Since layout_nicely() is the default layout algorithm for
plot(), most users were not even aware that they were using the FR or
DrL layouts behind the scenes. Now the policy is that layout_nicely()
attempts to get the job done without errors if possible, even if that means
that edge weights must be ignored. A warning is printed if this is the case.
Added:
reverse_edges() reverses specific or all edges in a graph.
Single-bracket indexing of V() and E() resolves attribute names in the
indexing expressions by default (for instance, E(g)[weight > x] matches
edges with a weight larger than a threshold). This can be problematic if the
attribute masks one of the variables in the local evaluation context.
We now have a pronoun called .env (similarly to rlang::.env) that
allows you to force attribute name lookup to the calling environment. For
sake of completeness, we also provide .data (similarly to rlang::.data)
to force attribute name lookup to the vertex / edge attributes only. These
pronouns are automatically injected into the environment where the indexing
expression is evaluated.
Deprecated:
V() or E() indexing start
with a dot since igraph 1.1.1; however, the old dotless names did not print
a deprecation warning so this may have gone unnoticed for years. We are
introducting a deprecation warning for nei(), innei(), outnei(),
inc(), from() and to() inside single-bracket indexing of vertex and
edge sequences and will remove the old variants soon.The C core is updated to 0.9.9, fixing a range of bugs.
Fixed:
communities objects is now reported correctly.layout_with_kk() would fail to produce reasonable results with the default initial
coordinates. This has been corrected, however, this function no longer produces
precisely the same output for a given graph as before. To restore the previous
behaviour, use layout_with_kk(g, coord=layout_in_circle(g)) in 2D or
layout_with_kk(g, dim=3, coord=layout_on_sphere(g)) in 3D.igraph.vs object with v[x, na_ok=T] now correctly handles the
na_ok argument in all cases; previous versions ignored it when x was
a single number.Other:
Fixed:
graph_from_adjacency_matrix() now works with sparse matrices even if the
cell values in the sparse matrix are unspecified.cluster_walktrap() when modularity=FALSE and membership=FALSE.cluster_walktrap() no longer accepts invalid weight vectors.cluster_walktrap() no longer returns a modularity vector of invalid length for
disconnected graphs. This also fixes some rare failures of this function on
weighted disconnected graphs.edge_attr() does not ignore its index=... argument any more.automorphisms(), automorphism_group() and canonical_permutation() now
allow all possible values supported by the C core in the sh argument.
Earlier versions supported only "fm".vertex.frame.width plotting parameter now allows zero and negative
values; these will simply remove the outline of the corresponding vertex.sh argument of the BLISS isomorphism algorithm in
isomorphic() was fixed; earlier versions incorrectly referred to sh1 and
sh2.dominator_tree() now conforms to its documentation with respect to the
dom component of the result: it contains the indices of the dominator
vertices for each vertex and -1 for the root of the dominator tree."power" algorithm of page_rank() have been removed from
the documentation, as this method is no longer available.The C core is updated to 0.9.7, fixing a range of bugs and introducing a number of new functions.
Added:
has_eulerian_path() and has_eulerian_cycle() decides whether there is an
Eulerian path or cycle in the graph.eulerian_path() and eulerian_cycle() returns the edges and vertices in an
Eulerian path or cycle in the graph.any_loop() checks whether a graph contains at least one loop edge.is_tree() checks whether a graph is a tree and also finds a possible rootto_prufer() converts a tree graph into its Prufer sequencemake_from_prufer() creates a tree graph from its Prufer sequencesample_tree() to sample labelled trees uniformly at randomsample_spanning_tree() to sample spanning trees of an undirected graph
uniformly at randomautomorphisms() and canonical_permutation() now supports vertex colorsrandom_edge_walk() to record the edges traversed during a random walkharmonic_centrality() calculates the harmonic centrality of vertices,
optionally with a cutoff on path lengthsmean_distance() now supports edge weights and it can also return the number
of unconnected vertex pairs when details=TRUE is passed as an argumentgreedy_vertex_coloring() finds vertex colorings based on a simple greedy
algorithm.bridges() finds the bridges (cut-edges) of a graphframe.width vertex attribute or the
vertex.frame.width keyword argument, thanks to @simoncarrignon .
See PR #500 for more details.automorphism_group() returns a possible (not necessarily minimal)
generating set of the automorphism group of a graph.global_efficiency() calculates the global efficiency of the graph.local_efficiency() calculates the local efficiency of each vertex in a graph.average_local_efficiency() calculates the average local efficiency across
the set of vertices in a graph.rewire(each_edge(...)) now supports rewiring only one endpoint of each edge.realize_degseq() generates graphs from degree sequences in a deterministic
manner. It is also available as make_(degseq(..., deterministic=TRUE)).clique_size_counts() counts cliques of different sizes without storing them all.feedback_arc_set() finds a minimum-weight feedback arc set in a graph, either
with an exact integer programming algorithm or with a linear-time approximation.make_bipartite_graph() now handles vertices with names.shortest_paths() now supports graphs with negative edge weights.min_cut() now supports s-t mincuts even if value.only=FALSE.as.matrix() now supports converting an igraph graph to an adjacency or edge
list matrix representation. See as.matrix.igraph() for more details. This
function was migrated from intergraph; thanks to Michal Bojanowski.Fixed:
is_connected() now returns FALSE for the null graphlength() on a graph now returns the number of vertices to make it
consistent with indexing the graph with [[.diameter() now corrently returns infinity for disconnected graphs when
unconnected=FALSE. Previous versions returned the number of vertices plus
one, which was clearly invalid for weighted graphs.mean_distance() now correctly treats the path length between disconnected
vertices as infinite when unconnected=FALSE. Previous versions used the
number of vertices plus one, adding a bias towards this number, even if the
graph was weighted and the number of vertices plus one was not a path length
that could safely have been considered as being longer than any "valid" path.layout_with_sugiyama() now handles the case of exactly one extra virtual
node correctly; fixes #85bfs() and dfs() callback functions now correctly receive 1-based vertex
indices and ranks; it used to be zero-based in earlier versionsbfs() or dfs() callback
does not crash R any moreprint() on a graph with a small max.lines value (smaller than the
number of lines needed to print the attribute list and the header) does not
raise an error any more; fixes #179as_adjacency_matrix(edges=TRUE, sparse=TRUE) now consistently returns the
last edge ID for each cell in the matrix instead of summing them.+ and - operators with a path() object consisting of two
vertices is now handled correctly; fixes #355topo_sort() now throws an error if the input graph is not acyclic instead
of returning an incorrect partial ordering.transitivity(mode="barrat") now
throw an error for multigraphs; the implementation does not work correctly
for multigraphs and earlier versions did not warn about this.Changed:
neimode argument of bfs() and dfs() was renamed to mode for sake
of consistency with other functions. The old argument name is deprecated and
will be removed in 1.4.0.bfs() and dfs() callback functions now correctly receive 1-based vertex
indices and ranks; it used to be zero-based in earlier versions. (This is
actually a bugfix so it's also mentioned in the "Fixed" section).closeness(), betweenness() and edge_betweenness() now all take a
cutoff argument on their own. estimate_closeness(), estimate_betweenness()
and estimate_edge_betweenness() became aliases, with identical signature.
They are not deprecated but their implementation might change in future
versions to provide proper estimation schemes instead of a simple cutoff-based
approximation. If you explicitly need cutoffs and you want your results to be
reproducible with future versions, use closeness(), betweenness() and
edge_betweenness() in your code with a cutoff argument.closeness() now only considers reachable vertices during the calculation;
in other words, closeness centrality is now calculated on a per-component
basis for disconnected graphs. Earlier versions considered all vertices.Deprecated:
cutoff=0 for closeness(), betweenness() and edge_betweenness()
is deprecated; if you want exact scores, use a negative cutoff. cutoff=0
will be interpreted literally from igraph 1.4.0.centr_degree_tmax() now prints a warning when it is invoked without an
explicit loops argument. loops will be mandatory from igraph 1.4.0.nexus_list(), nexus_info(), nexus_get() and nexus_search()
functions now return an error informing the user that the Nexus graph
repository has been taken offline (actually, several years ago). These
functions will be removed in 1.4.0.edges argument of as_adjacency_matrix() is deprecated; it will be
removed in igraph 1.4.0.Removed:
page_rank_old() function and the deprecated power method of
page_rank() were removed.Dec 27, 2021
No user visible changes.
Dec 14, 2021
Fixed:
igraph were accidentally built without GraphML
support on CRAN; this should now be fixed.Nov 22, 2021
No user visible changes.
Oct 26, 2021
No user visible changes.
Oct 15, 2021
The C core is updated to 0.8.5, fixing a range of bugs and introducing a number of new functions.
Added:
Fixed:
make_lattice() correctly rounds length to the nearest integer while
printing a warning (#115).make_empty_graph(NULL) now prints an error instead of producing an
invalid graph (#404).make_graph(c()) now produces an empty graph instead of printing a
misleading error message (#431).types argument of functions related to bipartite graphs now prints
a warning when the types are coerced to booleans (#476).layout_with_sugiyama() returns a layout of type matrix even if there is
only one vertex in the graph (#408).Deprecated:
membership argument of modularity.matrix() is now deprecated as the
function never needed it anyway.modularity() now prints a warning when it is applied on a directed graph
because the implementation in igraph's C core does not support directed
graphs as of version 0.8.5. The warning will be turned into an error in
the next minor (1.3.0) version of the R interface; the error will be removed
later when the C core is updated to a version that supports modularity for
directed networks.transitivity() now prints a warning when its local variant (type="local")
is called on a directed graph or a graph with multiple edges beecause the
implementation in the C core of igraph does not work reliably in these cases
as of version 0.8.5. The warning will be turned into an error in the next
minor (1.3.0) version of the R interface; the error will be removed later
when the C core is updated to a version that supports transitivity for
networks with multiple edges.Misc:
Oct 5, 2020
No user visible changes.
Mar 27, 2020
No user visible changes.
Feb 13, 2019
No user visible changes.
Jan 27, 2019
No user visible changes.
Jul 27, 2018
No user visible changes.
cluster_optimal() function does not work. Unfortunately we cannot
bundle the GLPK library into igraph on CRAN any more, because CRAN
maintainers forbid the pragmas in its source code.Jul 20, 2017
Jul 13, 2017
graph_id function was addededge_attr for some index valuesbfs() bug, restricted argument was zero-basedmatch_vertices is exported now%>% is re-exported in a better way, to avoid interference with other
packagesego_ functions default to order = 1 nowigraph_with_opt to run code with temporary igraph
options settingssample_asym_pref functioncurve_multiple to avoid warnings for graphs with self-loops.NMF package is only suggested now, it is not a hard
dependencypkgconfig package for options. This allows setting options
on a per-package basis. E.g. a package using igraph can set return.vs.es
to FALSE in its .onLoad() function, and then igraph will return
plain numeric vectors instead of vertex/edge sequences
if called from this package.igraph_options() returns the old values of the updated options,
this is actually useful, returning the new values was not.with_igraph_opt() function to temporarily change values of
igraph options.get.edge() is deprecated, use ends() instead. (This was already the case
for igraph 1.0.0, but we forgot to add a NEWS point for it.).Call(), to make native calls faster.anyNA() call, to be compatible with older R versions.head_of() and tail_of(), they were mixed up.label.dist independent of label lengths, fixes #63.R CMD check NOTEs.modularity().str.igraph() to print_all().V() or E() indexing
now begin with a dot. Old names are deprecated.
New names: .nei(), .innei(), .outnei(), .inc(), .from(),
.to(). #22layout_with_dh, layout_with_gem and
layout_with_sugiyama. They crashed in some cases.June 26, 2015
Some minor updates:
June 21, 2015
This is a new major version of igraph, and then why not call it 1.0.0. This does not mean that it is ready, it'll never be ready.
The biggest changes in the release are
make_() and make_graph() functions to
create graphs.make_graph() function to create graphs.layout_() (not the underscore!) function
to create graph layouts, see also add_layout_().upgrade_graph() on graphs created with previous igraph
versions.[[ operator now,
for easy viewing of vertex/edge metadata.as_ids() function to convert them to simple ids.layout_with_dh().layout_with_gem().mindist parameter for the
smallest distance to consider.all_simple_paths() function to list all simple paths in a graph.triangles() lists all triangles in a graph.local_scan() function calculates scan statistics.embed_adjacency_matrix() and embed_laplacian_matrix().*, the same graph multiple times. Can be also
used as rep().random_walk()adjacent_vertices() and incident_edges() functions,
they are vectorized, as opposed to neighhors() and incident().as_long_data_frame().Too many to list. Please try if your issue was fixed and (re-)report it if not. Thanks!
April 21, 2014
Some bug fixes, to make sure that the code included in 'Statistical Analysis of Network Data with R' works. See https://github.com/kolaczyk/sand
l,
not x, which is for complex attributes. Issue #578.communities objects, see create.communities().
Issue #547.constaint(), issue #580.simplify argument of graph.formula(), which was
broken, issue #586.crossing() adds better names to the result,
fixes issue #587.sir() function gives an error if the input graph is
not simple, fixes issue #582.February 4, 2014
There are a bunch of new features in the library itself, and other important changes in the life of the project. Thanks everyone for sending code and reporting bugs!
igraph's development has moved from Launchpad to github. This has actually happened several month ago, but never announced officially. The place for reporting bugs is at https://github.com/igraph/igraph/issues.
igraph's homepage is now hosted at http://igraph.org, and it is brand new. We wanted to make it easier to use and modern.
You can download nightly builds from igraph at http://igraph.org/nightly. Source and binary R packages (for windows and OSX), are all built.
demo(hrg).mod.matrix().layout.bipartite() function, a simple two-column layout
for bipartite graphs.barabasi.game(), algorithm psumtree-multiple
just froze.layout.mds() by default returns a layout matrix now.plot.communities() (plot.igraph(), really) draws a border
around the marked groups by default.name graph attribute to charactervertex.attriubutes(), graph.attributes() and edge.attributes().graph.disjoint.union() handles attributes now.graph.union() to handle attributes properly.rewire(): now supports the generation and destruction of loops.bipartite.random.game().get_shortest_paths(), reorganized the output of
get.shortest.paths() completely.graphlets() and related functions.bonpow() and alpha.centrality() and make sure that the
sparse solver is called.tkplot() news: enable setting coordinates from the command line
via tkplot.setcoords() and access to the canvas via
tkplot.canvas().igraph_edge_connectivity(), because of an
un-initialized variable in the C code.closeness() and related functions.bipartite.projection().graphNEL conversion functions only load the 'graph' package if it was
not loaded before and they load it at the end of the search path,
to minimize conflicts.graph.bfs() and graph.dfs().is.chordal().centralization.closeness.tmax().arpack() now gives error message if unknown options are
given.igraphtest() function.add.edges() does not allow now zeros in the vertex set.adjacent.triangles().graph.eigen() function, eigenproblems on adjacency matrices.decompose.graph() and graph.neighborhood() use it.
Fixes issue #508.optimal.community(), closes #511.graph.intersection.by.name(),
graph.union.by.name(), graph.difference.by.name().+ operator on graphs now calls graph.union() if both
argument graphs are named, and calls graph.disjoint.union()
otherwise.igraph.version().sbm.game().set.vertex/edge.attribute bug that changed both
graph objects, after copying (#533)barabasi.game that caused crashes.'which argument to bipartite.projection (#307).normalized argument to closeness functions, fixes issue #3.[[ on vertex/edge sets,
fixes #231.start argument in hrg.fit (#225).graph.density that resulted in incorrect values for
undirected graphs with loopsgraph.decompose), causing #550.graph.adjacency bugs for graphs with one edge,
and graphs with zero edges.graph.adjacency bug for undirected, weighted graphs and
sparse matrices.main, sub, xlab and ylab are proper graphics parameters
now (#555).graph.data.frame coerces arguments to data frame (#557).sir function.graph.mincut and related functions.graph.bfs (#575).Released Oct 28, 2013
Some bugs fixed:
Released May 16, 2013
Worked two CRAN check problems, and a gfortran bug (string bound checking does not work if code is called from C and without string length arguments at the "right" place).
Otherwise identical to 0.6.5-1.
Released February 27, 2013
Fixing an annoying bug, that broke two other packages on CRAN:
Released February 24, 2013
This is a minor release, to fix some very annoying bugs in 0.6.4:
Released February 2, 2013
The version number is not a mistake, we jump to 0.6.4 from 0.6, for technical reasons. This version was actually never really released, but some R packages of this version were uploaded to CRAN, so we include this version in this NEW file.
Added a vertex shape API for defining new vertex shapes, and also a couple of new vertex shapes.
Added the get.data.frame() function, opposite of graph.data.frame().
Added bipartite support to the Pajek reader and writer, closes bug #1042298.
degree.sequence.game() has a new method now: "simple_no_multiple".
Added the is.degree.sequence() and is.graphical.degree.sequence() functions.
rewire() has a new method: "loops", that can create loop edges.
Walktrap community detection now handles isolates.
layout.mds() returns a layout matrix now.
layout.mds() uses LAPACK instead of ARPACK.
Handle the '~' character in write.graph and read.graph. Bug #1066986.
Added k.regular.game().
Use vertex names to plot if no labels are specified in the function call or as vertex attributes. Fixes issue #1085431.
power.law.fit() can now use a C implementation.
Fixed a bug in barabasi.game() when out.seq was an empty vector.
Fixed a bug that made functions with a progress bar fail if called from another package.
Fixed a bug when creating graphs from a weighted integer adjacency matrix via graph.adjacency(). Bug #1019624.
Fixed overflow issues in centralization calculations.
Fixed a minimal.st.separators() bug, some vertex sets were incorrectly reported as separators. Bug #1033045.
Fixed a bug that mishandled vertex colors in VF2 isomorphism functions. Bug #1032819.
Pajek exporter now always quotes strings, thanks to Elena Tea Russo.
Fixed a bug with handling small edge weights in shortest paths calculation in shortest.paths() (Dijkstra's algorithm.) Thanks to Martin J Reed.
Weighted transitivity uses V(graph) as 'vids' if it is NULL.
Fixed a bug when 'pie' vertices were drawn together with other vertex shapes.
Speed up printing graphs.
Speed up attribute queries and other basic operations, by avoiding copying of the graph. Bug #1043616.
Fixed a bug in the NCV setting for ARPACK functions. It cannot be bigger than the matrix size.
layout.merge()'s DLA mode has better defaults now.
Fixed a bug in layout.mds() that resulted vertices on top of each other.
Fixed a bug in layout.spring(), it was not working properly.
Fixed layout.svd(), which was completely defunct.
Fixed a bug in layout.graphopt() that caused warnings and on some platforms crashes.
Fixed community.to.membership(). Bug #1022850.
Fixed a graph.incidence() crash if it was called with a non-matrix argument.
Fixed a get.shortest.paths bug, when output was set to "both".
Motif finding functions return NA for isomorphism classes that are not motifs (i.e. not connected). Fixes bug #1050859.
Fixed get.adjacency() when attr is given, and the attribute has some complex type. Bug #1025799.
Fixed attribute name in graph.adjacency() for dense matrices. Bug #1066952.
Fixed erratic behavior of alpha.centrality().
Fixed igraph indexing, when attr is given. Bug #1073705.
Fixed a bug when calculating the largest cliques of a directed graph. Bug #1073800.
Fixed a bug in the maximal clique search, closes #1074402.
Warn for negative weights when calculating PageRank.
Fixed dense, unweighted graph.adjacency when diag=FALSE. Closes issue #1077425.
Fixed a bug in eccentricity() and radius(), the results were often simply wrong.
Fixed a bug in get.all.shortest.paths() when some edges had zero weight.
graph.data.frame() is more careful when vertex names are numbers, to avoid their scientific notation. Fixes issue #1082221.
Better check for NAs in vertex names. Fixes issue #1087215
Fixed a potential crash in the DrL layout generator.
Fixed a bug in the Reingold-Tilford layout when the graph is directed and mode != ALL.
Released June 11, 2012
See also the release notes at http://igraph.sf.net/relnotes-0.6.html
Released November 22, 2009
Released April 10, 2009
See also the release notes at http://igraph.sf.net/relnotes-0.5.2.html
Released July 14, 2008
See also the release notes at http://igraph.sf.net/relnotes-0.5.1.html
Released February 14, 2008
See also the release notes at http://igraph.sf.net/relnotes-0.5.html
The 'rescale', 'asp' and 'frame' graphical parameters were added
Create graphs from a formula notation (graph.formula)
Handle graph attributes properly
Calculate the actual minimum cut for undirected graphs
Adjacency lists, get.adjlist and get.adjedgelist added
Eigenvector centrality computation is much faster now
Proper R warnings, instead of writing the warning to the terminal
R checks graphical parameters now, the unknown ones are not just ignored, but an error message is given
plot.igraph has an 'add' argument now to compose plots with multiple graphs
plot.igraph supports the 'main' and 'sub' arguments
layout.norm is public now, it can normalize a layout
It is possible to supply startup positions to layout generators
Always free memory when CTRL+C/ESC is pressed, in all operating systems
plot.igraph can plot square vertices now, see the 'shape' parameter
graph.adjacency rewritten when creating weighted graphs
We use match.arg whenever possible. This means that character scalar options can be abbreviated and they are always case insensitive
VF2 graph isomorphism routines can check subgraph isomorphism now, and they are able to return matching(s)
The BLISS graph isomorphism algorithm is included in igraph now. See canonical.permutation, graph.isomorphic.bliss
We use ARPACK for eigenvalue/eigenvector calculation. This means that the following functions were rewritten: page.rank, leading.eigenvector.community.*, evcent. New functions based on ARPACK: hub.score, authority.score, arpack.
Edge weights for Fruchterman-Reingold layout (layout.fruchterman.reingold).
Line graph calculation (line.graph)
Kautz and de Bruijn graph generators (graph.kautz, graph.de.bruijn)
Support for writing graphs in DOT format
Jaccard and Dice similarity coefficients added (similarity.jaccard, similarity.dice)
Counting the multiplicity of edges (count.multiple)
The graphopt layout algorithm was added, layout.graphopt
Generation of "famous" graphs (graph.famous).
Create graphs from LCF notation (graph.cf).
Dyad census and triad cencus functions (dyad.census, triad.census)
Cheking for simple graphs (is.simple)
Create full citation networks (graph.full.citation)
Create a histogram of path lengths (path.length.hist)
Forest fire model added (forest.fire.game)
DIMACS reader can handle different file types now
Biconnected components and articulation points (biconnected.components, articulation.points)
Kleinberg's hub and authority scores (hub.score, authority.score)
as.undirected handles attributes now
Geometric random graph generator (grg.game) can return the coordinates of the vertices
Function added to convert leading eigenvector community structure result to a membership vector (community.le.to.membership)
Weighted fast greedy community detection
Weighted page rank calculation
Functions for estimating closeness, betweenness, edge betweenness by introducing a cutoff for path lengths (closeness.estimate, betweenness.estimate, edge.betweenness.estimate)
Weighted modularity calculation
Function for permuting vertices (permute.vertices)
Betweenness and closeness calculations are speeded up
read.graph can handle all possible line terminators now (\r, \n, \r\n, \n\r)
Error handling was rewritten for walktrap community detection, the calculation can be interrupted now
The maxflow/mincut functions allow to supply NULL pointer for edge capacities, implying unit capacities for all edges
Released January 1, 2008
New:
Bug fixed:
Released October 3, 2007
This release should work seamlessly with the new R 2.6.0 version. Some other bugs were also fixed:
Released August 13, 2007
The next one in the sequence of bugfix releases. Thanks to many people sending bug reports. Here are the changes:
Released June 7, 2007
This is another bugfix release, as there was a serious bug in the R package of the previous version: it could not read and write graphs to files in any format under MS Windows.
Some other bits added:
Released May 23, 2007
This is a minor release, it corrects a number of bugs, mostly in the R package.
Released May 21, 2007
The major new additions in this release is a bunch of community detection algorithms and support for the GML file format. Here is the complete list of changes:
as the internal representation changed, graphs stored with 'save' with an older igraph version cannot be read back with the new version reliably.
neighbors returns ordered lists
is.loop and is.multiple were added
topological sorting
VF2 isomorphism algorithm
support for reading graphs from the Graph Database for isomorphism
graph.mincut can calculate the actual minimum cut
girth calculation added, thanks to Keith Briggs
support for reading and writing GML files
Walktrap community detection algorithm added, thanks to Matthieu Latapy and Pascal Pons
edge betweenness based community detection algorithm added
fast greedy algorithm for community detection by Clauset et al. added thanks to Aaron Clauset for sharing his code
leading eigenvector community detection algorithm by Mark Newman added
functions for creating dendrograms from the output of the community detection algorithms added
community.membership supporting function added, creates a membership vector from a community structure merge tree
modularity calculation added
graphics parameter handling is completely rewritten, uniform handling of colors and fonts, make sure you read ?igraph.plotting
new plotting parameter for edges: arrow.mode
a bug corrected when playing a nonlinear barabasi.game
better looking plotting in 3d using rglplot: edges are 3d too
rglplot layout is allowed to be two dimensional now
rglplot suspends updates while drawing, this makes it faster
loop edges are correctly plotted by all three plotting functions
better printing of attributes when printing graphs
summary of a graph prints attribute names
is.igraph rewritten to make it possible to inherit from the 'igraph' class
somewhat better looking progress meter for functions which support it
Released Dec 19, 2006
This is a new major release, it contains many new things:
Released Aug 23, 2006
This is a bug-fix release. Bugs fixed:
Released Aug 18, 2006
Release time at last! There are many new things in igraph 0.2, the most important ones:
New things specifically in the R package:
Although this release was somewhat tested on Linux, MS Windows, Mac OSX, Solaris 8 and FreeBSD, no heavy testing was done, so it might contain bugs, and we kindly ask you to send bug reports to make igraph better.
Released Jan 30, 2006
After about a year of development this is the first "official" release of the igraph library. This release should be considered as beta software, but it should be useful in general. Please send your questions and comments.