CHANGELOG: v1.2 New Functions, Changes, Bug Fixes New Functions: - $<-.network: replacement method for network objects. [CTB] - sum.network, prod.network: sums and products of multiple network objects. [CTB] Changes: - Direct assignments with network objects on the right-hand side now copy their right-hand argument (per standard R semantics). Originally, a pointer to the right-hand argument was copied (and network.copy was required for direct assignment). The direct use of network.copy is now unnecessary for most purposes, and should be avoided. [CTB] - network.density now allows explicit control of missing data behavior, support for ignoring "structural zeros" (per bipartite), and supports a wider range of hypergraphic cases. [CTB] - Some adjustments have been made to the overloading of network arithmetic operators, to ensure compatibility with future versions of R. Most importantly, the passing of an attrname argument to arithmetic operators is now defunct (since it violates the S3 generics). The addition of more general sum and prod methods hopefully make up for this regression. [CTB] - The network extraction and assignment operators now behave more like conventional matrices. In particular, single vectors are assumed to contain lists of cell indices (when given in isolation), and one-row, two-column matrices are treated as other two-column matrices. [CTB] - Various minor documentation and test file updates. [CTB] Bug Fixes: - as.matrix arguments have been modified to harmonize with the new R (2.5) generics definitions. [CTB] - Annoying but harmless tracer messages have been removed. [CTB] - Protection stack could overflow when large numbers of edges were deleted in a single call. [CTB; Submitted by Pavel Krivitsky] v1.1-2 Changes, Bug Fixes Changes: - getNeighborhood, getEdges, and getEdgeIDs (internal) now force type="combined" behavior on undirected networks; this was done at the R level before, but is now enforced in C as well. This is not generally user-level transparent, but affects the experimental network API [CTB] Bug Fixes: - as.network.matrix was not setting the bipartite attribute of the returned network properly, when called with a non-FALSE bipartite argument [MSH] - An error was present in some error return functions, causing errors on errors (which, happily, were only relevant when an error occurred) [CTB; Submitted by Skye Bender-deMoll] v1.1-1 New Functions, Changes New Functions: - The internal function setVertexAttribute has been added. This has no immediate user-level effect, but the new function is supported in the C API [CTB] Changes: - Use of the protection stack has been changed, so as to avoid racking up huge stacks when creating very large networks. This is expected to have a minimal impact on performance, but will avoid protection stack overflow issues in some cases [CTB] - A change in R 2.4.0 has apparently made it impossible for generic two-argument Ops (e.g., +,-,*) to dispatch to functions with more than two arguments. A side effect of this is that "+.network" and friends must be called with the full function name (as opposed to simply "+") when the optional attrname argument is being used. Note that this is not a change in the network package (although the test code has been updated to reflect it), but a regression due to R. Go complain to the R team [CTB] v1.1 New Features, Bug Fixes, Changes New Features: - [.network and [<-.network now allow the use of vertex names (where present) for selection of vertices [CTB] Bug Fixes: - add.vertices did not verify the integrity of vattr, and could generate a segfault if incorrectly called with a non-null, non-list value [CTB; reported by Skye Bender-deMoll] - as.network (and friends) could segfault if matrix.type was forced to adjacency while bipartite>0; new behavior essentially forces the use of the bipartite matrix method in this case [CTB] - delete.edges and set.edge.attribute returned an annoying (but harmless) warning when called with zero-length eid [CTB; reported by David Hunter] - delete.vertices did not adjust bipartite attribute (where present) to account for loss of mode 1 vertices [CTB] - get.vertex.attribute generated an error when called with na.omit=TRUE in some cases [CTB] - network.incidence could not be used to construct undirected dyadic networks [CTB] - set.vertex.attribute generated an error if called with attribute lists of length != network.size [CTB; reported by Skye Bender-deMoll] Changes: - Added a new overview man page (network-package) with information on how to get started with network [CTB] - [<-.network will now remove edges with zero values if both names.eval and add.edges are set, and will not add edges for those cells. Previously, the standard behavior was to add edges for all cells [CTB] - Added delete.edges to the "see also" for add.edges [CTB; suggested by Skye Bender-deMoll] - permute.vertexIDs now throws a warning when called with a cross-mode vertex exchange on a bipartite graph [CTB] - Default matrix type for as.matrix.network is now "adjacency," rather than the output of which.matrix.type(). Coercion methods should not have variable behavior depending on features such as network size, even if it is convenient for some purposes! The old behavior can be easily obtained via setting matrix.type=which.matrix.type(x), for those who want it [CTB] v1.0-1 Minor Bug Fixes, Changes Bug Fixes: - Various warnings were removed (apparently, these only appeared in R<2.1) [CTB] - plot.network was failing on networks where is.bipartite==TRUE [CTB] Changes: - The generic form of %c% was temporarily removed, to avoid namespace issues with sna. (This will be rectified in future releases.) [CTB] v1.0 New Functions, New Features, Changes, and Bug Fixes New Functions: - Operator overloading for +, -, *, |, &, and ! have been added, as has the composition operator, %c% [CTB] - Operator overloading is now supported for "[" and "[<-"; this allows network objects to be treated transparently as if they were adjacency matrices (in some cases, at least). New extraction/replacement operators %n%, %n%<-, %v%, %v%<- have been added for extracting/assigning values to network and vertex attributes (respectively) [CTB] - network.copy: returns a copy of the input network [CTB] - network.dyadcount: return the number of dyads in a network (optionally adjusting for the missing dyads) [MSH] New Features: - add.edges now checks for illegal loop-like edges when edge.check==TRUE [CTB] - get.neighborhood now allows users to specify whether missing edges should be ignored [CTB] - set.edge.value now accepts edge values in vector format [CTB] Changes: - All access access functions now modify their arguments in place; this greatly improves performance, but may produce unexpected behavior. If users wish to generate a modified copy of a network, they must first generate the copy and then modify it. Otherwise, the old object will be modified as well. In accordance with this, modification methods now return their (modified) arguments invisibly. [CTB] - Most access functions have now been backended; this has improved the performance of many operations by as much as two orders of magnitude [CTB] - get.edges and get.edgeIDs now treat all undirected networks as if called with neighborhood=="combined" [CTB] - as.matrix.network.incidence now handles undirected edges in a more conventional way [CTB] - network.adjacency will now ignore diagonal entries if has.loops=FALSE [CTB] Bug Fixes: - as.network.edgelist and as.network.incidence were producing spurious edge attributes [CTB] - list.edge.attributes generated failed under certain conditions (submitted by Matthew Wiener) [CTB] - set.edge.attribute was able to write attributes into non-existent (NULL) edges [CTB] - set.edge.value could exhibit strange behavior when carelessly chosen edge subsets were selected [CTB] v0.5-4 New Facilities for Bipartite, New Features, Changes, and Bug Fixes New Functions: - network.bipartite to store an explicit bipartite network. Modified network.initialize, etc, to accept "bipartite" argument. [MSH] - is.bipartite: logical test for a bipartite network [MSH] - read.paj: read one or more network objects from a Pajek file [MSH, DS] New Features: - summary.network now reports on edge attributes [MSH] Changes: - The composition operator (%c%) has been removed due to a name conflict with the sna package; since sna now supports network objects, its version can be used instead. [CTB] - as.sociomatrix is now properly configured to work in tandem with as.sociomatrix.sna (in the sna package). The functionality of the routine has also been extended slightly. [CTB] Bug Fixes: - .First.lib: Print out correct welcome banner for package [MSH] - Fix displayisolates determination in plot.network.default [MSH] v0.5-3 New Functions, New Data Set, and Changes New Functions: - permute.vertexIDs: Permute vertices in their internal representation [CTB] New Data: - emon: Drabek et al.'s Emergent Multi-organizational Networks [CTB] Changes: - The obsolete examples directory has been removed. [CTB] v0.5-2 New Features, New Functions and Bug Fixes New Functions: - delete.vertices: Remove one or more vertices (and associated edges) from a network object. - delete.edge.attribute, delete.network.attribute, delete.vertex attribute: Remove an edge/network/vertex attribute. - list.edge.attributes, list.network.attributes, list.vertex attributes: List all edge/network/vertex attribute names. New Features: - plot.graph.default now accepts vertex/edge attribute names for most vertex/edge display properties. Bug Fixes: - Edge deletion produced exciting and unexpected behavior in some cases. - network.initialize set vertex na attributes to TRUE by default.