Merge pull request #288 from stocnet/develop

v1.3.0

.Rbuildignore

@@ -15,3 +15,4 @@ vignettes/precompile\.R
 ^Meta$
 ^CRAN-SUBMISSION$
 ^README\.Rmd$
+^.mailmap$

.mailmap

@@ -0,0 +1 @@
+James Hollway <[email protected]> hollway <[email protected]>

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: migraph
-Title: Multimodal Network Analysis and More
-Version: 1.2.0
-Date: 2023-12-17
+Title: Many Network Measures, Motifs, Members, and Models
+Version: 1.3.0
+Date: 2024-01-24
 Description: A set of tools for analysing multimodal networks.
    It includes functions for measuring 
    centrality, centralization, cohesion, closure, constraint and diversity,
@@ -12,13 +12,13 @@ Description: A set of tools for analysing multimodal networks.
    Built on the 'manynet' package, all functions operate with matrices, edge lists, 
    and 'igraph', 'network', and 'tidygraph' objects,
    and on one-mode, two-mode (bipartite), and sometimes three-mode networks.
-URL: https://snlab-ch.github.io/migraph/
-BugReports: https://github.com/snlab-ch/migraph/issues
+URL: https://stocnet.github.io/migraph/
+BugReports: https://github.com/stocnet/migraph/issues
 License: MIT + file LICENSE
 Language: en-GB
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
 Depends:
     R (>= 3.6.0),
     manynet

NAMESPACE

@@ -2,10 +2,7 @@
 
 S3method(glance,netlm)
 S3method(glance,netlogit)
-S3method(plot,diff_model)
-S3method(plot,diffs_model)
 S3method(plot,graph_test)
-S3method(plot,learn_model)
 S3method(plot,matrix)
 S3method(plot,netlm)
 S3method(plot,netlogit)
@@ -14,24 +11,16 @@ S3method(plot,network_test)
 S3method(plot,node_measure)
 S3method(plot,node_member)
 S3method(plot,tie_measure)
-S3method(print,diff_model)
-S3method(print,diffs_model)
 S3method(print,graph_measure)
 S3method(print,graph_motif)
 S3method(print,graph_test)
-S3method(print,learn_model)
 S3method(print,network_measure)
 S3method(print,network_motif)
 S3method(print,network_test)
-S3method(print,node_mark)
 S3method(print,node_measure)
 S3method(print,node_member)
 S3method(print,node_motif)
-S3method(print,tie_mark)
 S3method(print,tie_measure)
-S3method(summary,diff_model)
-S3method(summary,diffs_model)
-S3method(summary,learn_model)
 S3method(summary,node_measure)
 S3method(summary,node_member)
 S3method(summary,node_motif)
@@ -43,7 +32,6 @@ export(.G)
 export(.N)
 export(aes)
 export(as.network)
-export(as_diffusion)
 export(bind_edges)
 export(cluster_concor)
 export(cluster_hierarchical)
@@ -87,9 +75,9 @@ export(graph_smallworld)
 export(graph_transitivity)
 export(graph_triad_census)
 export(guides)
-export(is.igraph)
 export(is.network)
 export(is.tbl_graph)
+export(is_igraph)
 export(k_elbow)
 export(k_silhouette)
 export(k_strict)
@@ -100,6 +88,7 @@ export(network_assortativity)
 export(network_balance)
 export(network_betweenness)
 export(network_brokerage_census)
+export(network_change)
 export(network_closeness)
 export(network_cohesion)
 export(network_components)
@@ -134,6 +123,8 @@ export(network_richclub)
 export(network_richness)
 export(network_scalefree)
 export(network_smallworld)
+export(network_spatial)
+export(network_stability)
 export(network_transitivity)
 export(network_transmissibility)
 export(network_triad_census)
@@ -151,6 +142,7 @@ export(node_constraint)
 export(node_core)
 export(node_coreness)
 export(node_cuts)
+export(node_deg)
 export(node_degree)
 export(node_diversity)
 export(node_eccentricity)
@@ -161,41 +153,36 @@ export(node_eigenvector)
 export(node_equivalence)
 export(node_exposure)
 export(node_fast_greedy)
+export(node_flow)
+export(node_fluid)
 export(node_harmonic)
 export(node_heterophily)
 export(node_hierarchy)
 export(node_homophily)
 export(node_indegree)
+export(node_induced)
 export(node_infection_length)
 export(node_infomap)
-export(node_is_core)
-export(node_is_cutpoint)
-export(node_is_exposed)
-export(node_is_fold)
-export(node_is_infected)
-export(node_is_isolate)
-export(node_is_latent)
-export(node_is_max)
-export(node_is_mentor)
-export(node_is_min)
-export(node_is_random)
-export(node_is_recovered)
+export(node_information)
 export(node_kernighanlin)
 export(node_leading_eigen)
 export(node_leiden)
 export(node_louvain)
+export(node_multidegree)
 export(node_neighbours_degree)
 export(node_optimal)
 export(node_outdegree)
 export(node_pagerank)
 export(node_path_census)
+export(node_posneg)
 export(node_power)
 export(node_quad_census)
 export(node_reach)
 export(node_reciprocity)
 export(node_redundancy)
 export(node_regular_equivalence)
 export(node_richness)
+export(node_roulette)
 export(node_spinglass)
 export(node_strong_components)
 export(node_structural_equivalence)
@@ -207,10 +194,6 @@ export(node_walktrap)
 export(node_weak_components)
 export(over_time)
 export(over_waves)
-export(play_diffusion)
-export(play_diffusions)
-export(play_learning)
-export(play_segregation)
 export(rename)
 export(test_gof)
 export(test_permutation)
@@ -221,20 +204,13 @@ export(tie_closeness)
 export(tie_cohesion)
 export(tie_degree)
 export(tie_eigenvector)
-export(tie_is_bridge)
-export(tie_is_loop)
-export(tie_is_max)
-export(tie_is_min)
-export(tie_is_multiple)
-export(tie_is_reciprocated)
 export(with_graph)
 export(xlab)
 export(ylab)
 import(tidygraph)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,bind_cols)
 importFrom(dplyr,left_join)
-importFrom(dplyr,tibble)
 importFrom(furrr,furrr_options)
 importFrom(furrr,future_map_dfr)
 importFrom(future,plan)
@@ -243,7 +219,6 @@ importFrom(generics,tidy)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,element_blank)
 importFrom(ggplot2,element_text)
-importFrom(ggplot2,geom_histogram)
 importFrom(ggplot2,geom_hline)
 importFrom(ggplot2,geom_tile)
 importFrom(ggplot2,geom_vline)
@@ -262,44 +237,40 @@ importFrom(ggplot2,ylab)
 importFrom(igraph,V)
 importFrom(igraph,adhesion)
 importFrom(igraph,alpha_centrality)
-importFrom(igraph,articulation_points)
 importFrom(igraph,assortativity_degree)
 importFrom(igraph,cohesion)
 importFrom(igraph,components)
-importFrom(igraph,decompose)
 importFrom(igraph,degree)
-importFrom(igraph,delete.edges)
 importFrom(igraph,delete_vertices)
 importFrom(igraph,diameter)
 importFrom(igraph,distances)
 importFrom(igraph,eccentricity)
 importFrom(igraph,edge_betweenness)
 importFrom(igraph,edge_density)
 importFrom(igraph,fit_power_law)
-importFrom(igraph,graph.neighborhood)
 importFrom(igraph,graph_from_incidence_matrix)
-importFrom(igraph,is.igraph)
 importFrom(igraph,is_bipartite)
+importFrom(igraph,is_igraph)
 importFrom(igraph,knn)
+importFrom(igraph,make_ego_graph)
 importFrom(igraph,mean_distance)
 importFrom(igraph,power_centrality)
 importFrom(igraph,reciprocity)
 importFrom(igraph,transitivity)
 importFrom(igraph,triad_census)
 importFrom(igraph,vcount)
-importFrom(igraph,which_loop)
-importFrom(igraph,which_multiple)
-importFrom(igraph,which_mutual)
 importFrom(manynet,as_igraph)
 importFrom(network,as.network)
 importFrom(network,is.network)
 importFrom(purrr,flatten)
+importFrom(rlang,"%||%")
 importFrom(rlang,.data)
-importFrom(rlang,`%||%`)
 importFrom(rlang,enquo)
 importFrom(rlang,eval_tidy)
 importFrom(sna,brokerage)
+importFrom(sna,flowbet)
 importFrom(sna,gcor)
+importFrom(sna,infocent)
 importFrom(stats,as.dist)
 importFrom(stats,as.formula)
 importFrom(stats,binomial)

NEWS.md

@@ -1,3 +1,52 @@
+# migraph 1.3.0
+
+2024-01-24
+
+## Package
+
+- Migrated package repository to 'stocnet' organisation
+- Significant documentation updates
+
+## Marks
+
+- Migrated remaining marks functions to `{manynet}`
+
+## Measures
+
+- Added `network_change()` to measure the Hamming distance between two or more networks
+- Added `network_stability()` to measure the Jaccard index between two or more networks
+- Added `network_spatial()` to measure spatial association (Moran's I, closes #209)
+- Added `node_deg()` for a non-normalised version of `node_degree()`
+- `node_degree()` now normalises strength centrality
+- Added `node_induced()` to measure nodes' induced betweenness centralities
+- Added `node_flow()` to measure nodes' flow betweenness centralities (closes #195)
+- Added `node_information()` to measure nodes' information or current-flow closeness centralities (closes #194)
+- Added `node_multidegree()` to measure the ratio of one type of tie in a multiplex network to another
+- Added `node_posneg()` measures the PN centrality of signed networks
+
+## Members
+
+- Fixed #287 by making `node_tie_census()` and `node_triad_census()` work with the new multiplex format in `{manynet}` (which relies on a "type" tie attribute rather than multiple tie attributes)
+  - This restores functionality to `node_structural_equivalence()` and `node_regular_equivalence()`
+  - Incidental speed improvements
+- Added `node_fluid()` community detection algorithm
+- Added `node_roulette()` for identifying groups of nodes that haven't interacted before
+
+## Models
+
+- Migrated `play_*()` functions to `{manynet}`, including `as_diffusion()` and the diffusion tutorial
+- Added specification advice to `network_reg()` so that specifications that include a 'sim' or 'same' effect for a variable are encouraged to also include more elementary 'ego' and 'alter' effects
+- `network_reg()` now ignores the LHS of the formula for uniplex networks
+
+
+# migraph 1.2.1
+
+2023-12-17
+
+## Measures
+
+- Fixed documentation issues in `node_adoption_time()`
+
 # migraph 1.2.0
 
 2023-12-17