Merge pull request #105 from stocnet/develop

v1.4.0

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: manynet
 Title: Many Ways to Make, Modify, Map, Mark, and Measure Myriad Networks
-Version: 1.3.3
-Date: 2024-11-10
+Version: 1.4.0
+Date: 2024-12-06
 Description: Many tools for making, modifying, mapping, marking, measuring, 
    and motifs and memberships of many different types of networks.
    All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects,
@@ -29,8 +29,6 @@ Imports:
 Suggests:
     BiocManager,
     concaveman,
-    future,
-    furrr,
     gganimate,
     ggdendro,
     ggforce,

NAMESPACE

@@ -7,10 +7,12 @@ S3method(add_nodes,tbl_graph)
 S3method(add_ties,igraph)
 S3method(add_ties,network)
 S3method(add_ties,tbl_graph)
+S3method(as_changelist,tbl_graph)
 S3method(as_diffnet,diff_model)
 S3method(as_diffusion,diff_model)
 S3method(as_diffusion,diffnet)
 S3method(as_diffusion,igraph)
+S3method(as_diffusion,mnet)
 S3method(as_edgelist,data.frame)
 S3method(as_edgelist,igraph)
 S3method(as_edgelist,matrix)
@@ -32,6 +34,7 @@ S3method(as_igraph,igraph)
 S3method(as_igraph,matrix)
 S3method(as_igraph,network)
 S3method(as_igraph,network.goldfish)
+S3method(as_igraph,networkDynamic)
 S3method(as_igraph,siena)
 S3method(as_igraph,tbl_graph)
 S3method(as_matrix,data.frame)
@@ -61,6 +64,7 @@ S3method(as_tidygraph,list)
 S3method(as_tidygraph,matrix)
 S3method(as_tidygraph,network)
 S3method(as_tidygraph,network.goldfish)
+S3method(as_tidygraph,networkDynamic)
 S3method(as_tidygraph,siena)
 S3method(as_tidygraph,tbl_graph)
 S3method(delete_nodes,igraph)
@@ -118,6 +122,7 @@ S3method(is_weighted,igraph)
 S3method(is_weighted,matrix)
 S3method(is_weighted,network)
 S3method(is_weighted,tbl_graph)
+S3method(mutate_changes,tbl_graph)
 S3method(mutate_nodes,igraph)
 S3method(mutate_nodes,tbl_graph)
 S3method(na_to_mean,data.frame)
@@ -134,6 +139,7 @@ S3method(net_dims,data.frame)
 S3method(net_dims,igraph)
 S3method(net_dims,matrix)
 S3method(net_dims,network)
+S3method(pillar_shaft,logi)
 S3method(plot,diff_model)
 S3method(plot,diffs_model)
 S3method(plot,learn_model)
@@ -156,6 +162,8 @@ S3method(print,node_member)
 S3method(print,node_motif)
 S3method(print,tie_mark)
 S3method(print,tie_measure)
+S3method(select_nodes,igraph)
+S3method(select_nodes,tbl_graph)
 S3method(summary,diff_model)
 S3method(summary,diffs_model)
 S3method(summary,learn_model)
@@ -272,6 +280,7 @@ S3method(to_ties,igraph)
 S3method(to_ties,matrix)
 S3method(to_ties,network)
 S3method(to_ties,tbl_graph)
+S3method(to_time,tbl_graph)
 S3method(to_twomode,igraph)
 S3method(to_twomode,network)
 S3method(to_twomode,tbl_graph)
@@ -311,13 +320,16 @@ export("%>%")
 export(.E)
 export(.G)
 export(.N)
+export(add_changes)
 export(add_info)
 export(add_node_attribute)
 export(add_nodes)
 export(add_tie_attribute)
 export(add_ties)
 export(aes)
+export(apply_changes)
 export(arrange_ties)
+export(as_changelist)
 export(as_diffnet)
 export(as_diffusion)
 export(as_edgelist)
@@ -337,6 +349,7 @@ export(clear_glossary)
 export(cluster_concor)
 export(cluster_cosine)
 export(cluster_hierarchical)
+export(collect_changes)
 export(create_components)
 export(create_core)
 export(create_degree)
@@ -352,6 +365,7 @@ export(create_tree)
 export(delete_nodes)
 export(delete_ties)
 export(extract_tute)
+export(filter_changes)
 export(filter_nodes)
 export(filter_ties)
 export(from_egos)
@@ -381,6 +395,7 @@ export(is.tbl_graph)
 export(is_acyclic)
 export(is_aperiodic)
 export(is_attributed)
+export(is_changing)
 export(is_complex)
 export(is_connected)
 export(is_directed)
@@ -421,6 +436,8 @@ export(layout_tbl_graph_tetrad)
 export(layout_tbl_graph_triad)
 export(many_palettes)
 export(mutate)
+export(mutate_changes)
+export(mutate_net)
 export(mutate_nodes)
 export(mutate_ties)
 export(na_to_mean)
@@ -431,6 +448,7 @@ export(net_balance)
 export(net_betweenness)
 export(net_by_brokerage)
 export(net_by_dyad)
+export(net_by_hazard)
 export(net_by_mixed)
 export(net_by_quad)
 export(net_by_tetrad)
@@ -476,11 +494,14 @@ export(net_scalefree)
 export(net_smallworld)
 export(net_spatial)
 export(net_stability)
+export(net_strength)
 export(net_tie_attributes)
 export(net_ties)
+export(net_toughness)
 export(net_transitivity)
 export(net_transmissibility)
 export(net_upperbound)
+export(net_waves)
 export(network_adhesion)
 export(network_assortativity)
 export(network_balance)
@@ -613,6 +634,7 @@ export(node_is_infected)
 export(node_is_isolate)
 export(node_is_latent)
 export(node_is_max)
+export(node_is_mean)
 export(node_is_mentor)
 export(node_is_min)
 export(node_is_mode)
@@ -654,14 +676,11 @@ export(node_triad_census)
 export(node_vitality)
 export(node_walktrap)
 export(node_weak_components)
-export(over_membership)
-export(over_time)
-export(over_waves)
 export(pkg_data)
 export(play_diffusion)
-export(play_diffusions)
 export(play_learning)
 export(play_segregation)
+export(print_all)
 export(print_glossary)
 export(read_cran)
 export(read_dynetml)
@@ -707,6 +726,9 @@ export(scale_fill_rug)
 export(scale_fill_sdgs)
 export(scale_fill_uzh)
 export(scale_size)
+export(select)
+export(select_changes)
+export(select_nodes)
 export(select_ties)
 export(set_manynet_theme)
 export(summarise_ties)
@@ -768,6 +790,7 @@ export(to_slices)
 export(to_subgraph)
 export(to_subgraphs)
 export(to_ties)
+export(to_time)
 export(to_tree)
 export(to_twomode)
 export(to_undirected)
@@ -947,6 +970,7 @@ importFrom(network,list.edge.attributes)
 importFrom(network,network.size)
 importFrom(network,read.paj)
 importFrom(network,set.vertex.attribute)
+importFrom(pillar,pillar_shaft)
 importFrom(pillar,style_subtle)
 importFrom(pillar,tbl_format_body)
 importFrom(pillar,tbl_format_setup)
@@ -969,6 +993,7 @@ importFrom(tidygraph,mutate)
 importFrom(tidygraph,node_is_isolated)
 importFrom(tidygraph,rename)
 importFrom(tidygraph,reroute)
+importFrom(tidygraph,select)
 importFrom(tidygraph,tbl_graph)
 importFrom(tidygraph,to_subgraph)
 importFrom(tidygraph,with_graph)

NEWS.md

@@ -1,3 +1,72 @@
+# manynet 1.4.0
+
+## Making
+
+- Updated documentation on "mnet" class objects
+- Improved `print.mnet()` to print sections more prettily and 
+accommodate changes when present
+- Added `print_all()` for printing infinite rows
+- Moved `play_diffusions()` to `{migraph}` (but not `play_diffusion()`)
+- Improved `play_diffusion()` to return an 'mnet' class object with changes
+instead of a 'diff_model' object with hidden network
+  - Older behavior can still be obtained using `old_version = TRUE`
+- Improved `write_*()` functions by printing picked pathnames to the console
+
+## Modifying
+
+- Added `as_changelist()` for extracting changelists from 'mnet' objects
+- Added `as_diffusion.mnet()` for maintaining backward compatibility for
+diffusion measures
+- Added `as_tidygraph.networkDynamic()` and `as_igraph.networkDynamic()` for 
+coercing 'networkDynamic' objects into 'mnet', 'tidygraph', and 'igraph' objects
+- Added functions for adding and working with network changes, i.e. changes to network nodes
+  - Added `add_changes()` for adding changes to a network,
+  including checks and imputing activity and susceptibility
+  - Added `mutate_changes()` to mutate changes
+  - Added `select_changes()` to select change variables
+  - Added `filter_changes()` to filter changes
+  - Added `collect_changes()` to collect changes up to a time point
+  - Added `apply_changes()` to apply collected changes to a time point
+- Added `to_time()` for scoping a longitudinal network to a time point,
+including nodal and/or tie changes 
+- Added `select_nodes()` for selecting only some nodal variables
+- Added `mutate_net()` for working with network information
+
+## Marking
+
+- Added `is_changing()` for identifying networks with a change component
+- Added `node_is_mean()` for identifying typical nodes
+- Updated `node_is_*()` diffusion marks to work with new .data output
+- Internally added expect_mark test helper
+
+## Measuring
+
+- Added `net_strength()` for measuring the number of ties that would need to be
+removed from a network to increase its number of components
+- Added `net_toughness()` for measuring the number of nodes that would need to be
+removed from a network to increase its number of components
+- Moved `over_*()` to `{migraph}`
+- Updated `node_*()` diffusion measures to work with new .data output
+- Improved `net_modularity()` by informing users when a bipartition is used
+- Added `net_waves()` for measuring the number of waves in a network
+
+## Motifs
+
+- Renamed `net_hazard()` to `net_by_hazard()`
+- Updated `node_by_*()` diffusion motifs to work with new .data output
+
+## Data
+
+- Updated `fict_potter` with composition changes
+- Renamed `ison_starwars` to `fict_starwars`, updating it with composition changes and additional coding
+- Added `irps_911` network data on 9/11 hijackers and associates
+
+## Learning
+
+- Updated 'community' tutorial with guidance on `node_in_community()`
+- Updated 'position' tutorial with guidance on `tie_is_bridge()` and `node_bridges()`
+- Moved 'diffusion' tutorial to `{migraph}` to help with dependencies
+
 # manynet 1.3.3
 
 ## Modifying