Merge branch 'develop' into ggplot2_3.5.0

Author: henriquesposito

.Rbuildignore

@@ -17,3 +17,4 @@ vignettes/precompile\.R
 ^Meta$
 ^CRAN-SUBMISSION$
 ^README\.Rmd$
+^.mailmap$

.mailmap

@@ -0,0 +1 @@
+James Hollway <james.hollway@graduateinstitute.ch> hollway <hollway@MA0359.local>

DESCRIPTION

@@ -1,27 +1,28 @@
 Package: manynet
-Title: Many Ways to Make, Modify, and Map Myriad Networks
-Version: 0.3.1
-Date: 2023-12-17
-Description: A set of tools for making, modifying, and mapping many different types of networks.
+Title: Many Ways to Make, Modify, Mark, and Map Myriad Networks
+Version: 1.0.0
+Date: 2024-01-24
+Description: A set of tools for making, modifying, marking, and mapping many different types of networks.
    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.
    The package includes functions for importing and exporting, creating and generating networks,
-   molding and manipulating networks and node and tie attributes,
+   modifying networks and node and tie attributes,
    and describing and visualizing networks with sensible defaults.
-URL: https://snlab-ch.github.io/manynet/
-BugReports: https://github.com/snlab-ch/manynet/issues
+URL: https://stocnet.github.io/manynet/
+BugReports: https://github.com/stocnet/manynet/issues
 Depends: R (>= 3.6.0)
 License: MIT + file LICENSE
 Language: en-GB
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
 Imports: 
     dplyr (>= 1.1.0),
     ggplot2,
     ggraph,
     igraph (>= 1.6.0),
     network,
+    pillar,
     tidygraph
 Suggests: 
     BiocManager,
@@ -43,8 +44,10 @@ Suggests:
     rmarkdown,
     roxygen2,
     RSiena,
-    testthat,
-    xml2
+    testthat (>= 3.0.0),
+    xml2,
+    future,
+    furrr
 Enhances:
     Rgraphviz
 Authors@R: 
@@ -59,3 +62,6 @@ Authors@R:
              comment = c("IHEID", ORCID = "0000-0003-3420-6085"))
     )
 Roxygen: list(markdown = TRUE, roclets = c("namespace", "rd"))
+Config/testthat/parallel: true
+Config/testthat/edition: 3
+Config/testthat/start-first: mark_is 

NAMESPACE

@@ -54,6 +54,7 @@ S3method(as_tidygraph,network.goldfish)
 S3method(as_tidygraph,siena)
 S3method(as_tidygraph,tbl_graph)
 S3method(delete_nodes,igraph)
+S3method(delete_ties,igraph)
 S3method(is_complex,data.frame)
 S3method(is_complex,igraph)
 S3method(is_complex,matrix)
@@ -115,7 +116,19 @@ S3method(network_dims,data.frame)
 S3method(network_dims,igraph)
 S3method(network_dims,matrix)
 S3method(network_dims,network)
+S3method(plot,diff_model)
+S3method(plot,diffs_model)
+S3method(plot,learn_model)
+S3method(print,diff_model)
+S3method(print,diffs_model)
+S3method(print,learn_model)
+S3method(print,node_mark)
 S3method(print,tbl_graph)
+S3method(print,tie_mark)
+S3method(summary,diff_model)
+S3method(summary,diffs_model)
+S3method(summary,learn_model)
+S3method(to_acyclic,data.frame)
 S3method(to_acyclic,igraph)
 S3method(to_acyclic,matrix)
 S3method(to_acyclic,network)
@@ -256,6 +269,7 @@ export(add_tie_attribute)
 export(add_ties)
 export(aes)
 export(as.network)
+export(as_diffusion)
 export(as_edgelist)
 export(as_graphAM)
 export(as_igraph)
@@ -266,8 +280,8 @@ export(as_tidygraph)
 export(autographd)
 export(autographr)
 export(autographs)
-export(bind_edges)
 export(bind_node_attributes)
+export(bind_ties)
 export(create_components)
 export(create_core)
 export(create_empty)
@@ -278,11 +292,14 @@ export(create_ring)
 export(create_star)
 export(create_tree)
 export(delete_nodes)
+export(delete_ties)
 export(extract_tute)
+export(filter_nodes)
 export(filter_ties)
 export(from_egos)
 export(from_slices)
 export(from_subgraphs)
+export(from_ties)
 export(from_waves)
 export(generate_permutation)
 export(generate_random)
@@ -293,7 +310,6 @@ export(ggplot)
 export(ggsave)
 export(ggtitle)
 export(guides)
-export(is.igraph)
 export(is.network)
 export(is.tbl_graph)
 export(is_acyclic)
@@ -305,7 +321,9 @@ export(is_dynamic)
 export(is_edgelist)
 export(is_eulerian)
 export(is_graph)
+export(is_igraph)
 export(is_labelled)
+export(is_list)
 export(is_longitudinal)
 export(is_manynet)
 export(is_multiplex)
@@ -328,6 +346,7 @@ export(layout_tbl_graph_railway)
 export(layout_tbl_graph_triad)
 export(many_palettes)
 export(mutate)
+export(mutate_nodes)
 export(mutate_ties)
 export(na_to_mean)
 export(na_to_zero)
@@ -337,8 +356,25 @@ export(network_nodes)
 export(network_tie_attributes)
 export(network_ties)
 export(node_attribute)
+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_mode)
 export(node_names)
+export(pkg_data)
+export(play_diffusion)
+export(play_diffusions)
+export(play_learning)
+export(play_segregation)
 export(read_dynetml)
 export(read_edgelist)
 export(read_graphml)
@@ -347,6 +383,7 @@ export(read_nodelist)
 export(read_pajek)
 export(read_ucinet)
 export(rename)
+export(rename_nodes)
 export(rename_ties)
 export(run_tute)
 export(scale_color_centres)
@@ -361,6 +398,18 @@ export(scale_colour_iheid)
 export(scale_colour_rug)
 export(scale_colour_sdgs)
 export(scale_colour_uzh)
+export(scale_edge_color_centres)
+export(scale_edge_color_ethz)
+export(scale_edge_color_iheid)
+export(scale_edge_color_rug)
+export(scale_edge_color_sdgs)
+export(scale_edge_color_uzh)
+export(scale_edge_colour_centres)
+export(scale_edge_colour_ethz)
+export(scale_edge_colour_iheid)
+export(scale_edge_colour_rug)
+export(scale_edge_colour_sdgs)
+export(scale_edge_colour_uzh)
 export(scale_fill_centres)
 export(scale_fill_ethz)
 export(scale_fill_iheid)
@@ -374,6 +423,14 @@ export(theme_iheid)
 export(theme_rug)
 export(theme_uzh)
 export(tie_attribute)
+export(tie_is_bridge)
+export(tie_is_feedback)
+export(tie_is_loop)
+export(tie_is_max)
+export(tie_is_min)
+export(tie_is_multiple)
+export(tie_is_random)
+export(tie_is_reciprocated)
 export(tie_signs)
 export(tie_weights)
 export(to_acyclic)
@@ -400,6 +457,7 @@ export(to_slices)
 export(to_subgraph)
 export(to_subgraphs)
 export(to_ties)
+export(to_tree)
 export(to_twomode)
 export(to_undirected)
 export(to_uniplex)
@@ -431,9 +489,11 @@ importFrom(dplyr,mutate)
 importFrom(dplyr,rename)
 importFrom(dplyr,select)
 importFrom(dplyr,summarise)
+importFrom(dplyr,tibble)
 importFrom(dplyr,ungroup)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,arrow)
+importFrom(ggplot2,geom_histogram)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,geom_segment)
 importFrom(ggplot2,geom_text)
@@ -456,19 +516,20 @@ importFrom(ggraph,geom_node_label)
 importFrom(ggraph,geom_node_point)
 importFrom(ggraph,geom_node_text)
 importFrom(ggraph,get_con)
-importFrom(ggraph,ggraph)
 importFrom(ggraph,scale_edge_width_continuous)
 importFrom(igraph,E)
 importFrom(igraph,V)
 importFrom(igraph,add_edges)
 importFrom(igraph,add_vertices)
+importFrom(igraph,any_loop)
 importFrom(igraph,any_multiple)
+importFrom(igraph,articulation_points)
 importFrom(igraph,as.directed)
 importFrom(igraph,as.undirected)
 importFrom(igraph,as_adjacency_matrix)
 importFrom(igraph,as_biadjacency_matrix)
 importFrom(igraph,as_data_frame)
-importFrom(igraph,bipartite.projection)
+importFrom(igraph,bipartite_projection)
 importFrom(igraph,complementer)
 importFrom(igraph,decompose)
 importFrom(igraph,degree)
@@ -479,23 +540,22 @@ importFrom(igraph,delete_vertices)
 importFrom(igraph,edge_attr)
 importFrom(igraph,edge_attr_names)
 importFrom(igraph,eulerian_path)
+importFrom(igraph,feedback_arc_set)
 importFrom(igraph,get.edgelist)
-importFrom(igraph,get.vertex.attribute)
 importFrom(igraph,graph_from_adjacency_matrix)
 importFrom(igraph,graph_from_biadjacency_matrix)
 importFrom(igraph,graph_from_data_frame)
 importFrom(igraph,gsize)
+importFrom(igraph,has_eulerian_path)
 importFrom(igraph,induced_subgraph)
-importFrom(igraph,is.connected)
-importFrom(igraph,is.directed)
-importFrom(igraph,is.igraph)
-importFrom(igraph,is.loop)
-importFrom(igraph,is.named)
-importFrom(igraph,is.simple)
-importFrom(igraph,is.weighted)
 importFrom(igraph,is_bipartite)
+importFrom(igraph,is_connected)
 importFrom(igraph,is_dag)
-importFrom(igraph,list.vertex.attributes)
+importFrom(igraph,is_directed)
+importFrom(igraph,is_igraph)
+importFrom(igraph,is_named)
+importFrom(igraph,is_simple)
+importFrom(igraph,is_weighted)
 importFrom(igraph,make_ego_graph)
 importFrom(igraph,make_lattice)
 importFrom(igraph,make_line_graph)
@@ -515,6 +575,9 @@ importFrom(igraph,simplify)
 importFrom(igraph,vcount)
 importFrom(igraph,vertex_attr)
 importFrom(igraph,vertex_attr_names)
+importFrom(igraph,which_loop)
+importFrom(igraph,which_multiple)
+importFrom(igraph,which_mutual)
 importFrom(igraph,write_graph)
 importFrom(network,as.edgelist)
 importFrom(network,as.matrix.network)
@@ -529,13 +592,17 @@ importFrom(network,list.edge.attributes)
 importFrom(network,network.size)
 importFrom(network,read.paj)
 importFrom(network,set.vertex.attribute)
+importFrom(pillar,style_subtle)
+importFrom(pillar,tbl_format_body)
+importFrom(pillar,tbl_format_setup)
 importFrom(stats,cor)
 importFrom(tidygraph,.E)
 importFrom(tidygraph,.G)
 importFrom(tidygraph,.N)
 importFrom(tidygraph,activate)
 importFrom(tidygraph,as_tbl_graph)
 importFrom(tidygraph,bind_edges)
+importFrom(tidygraph,filter)
 importFrom(tidygraph,is.tbl_graph)
 importFrom(tidygraph,mutate)
 importFrom(tidygraph,node_is_isolated)

NEWS.md

@@ -1,3 +1,71 @@
+# manynet 1.0.0
+
+2023-12-24
+
+## Package
+
+- Major overhaul of documentation
+  - Moved function description up so that it appears in tooltips
+  - Split documentation of many functions to provide more space for explanation
+  - Moved some functions around for more thematic documentation
+- Added `pkg_data()` to report an overview of data contained within the package(s)
+- Updated README and DESCRIPTION with new organisational affiliation: stocnet/manynet
+
+## Making
+
+- Migrated `play_diffusion()` and `play_diffusions()` from `{migraph}`
+  - Including class creation, and `print()`, `summary()`, and `plot()` methods
+- Migrated `play_learning()` and `play_segregation()` from `{migraph}`
+  - Including class creation, and `print()`, `summary()`, and `plot()` methods
+- Fixed bug in `create_tree()` where it was not returning a two-mode network correctly
+
+## Modifying
+
+- Added `as_diffusion()` to coerce a table of diffusion events into diff_model class
+  - `as_*()` functions are now considered modifications
+- Completed a full range of tidy verbs for nodes
+  - Added `mutate_nodes()`
+  - Added `filter_nodes()`
+  - Added `rename_nodes()`
+- Completed a full range of tidy and igraph verbs for ties
+  - Added `bind_ties()`
+  - Added `delete_ties()`
+- Added `to_tree()` to find one or more spanning trees amongst a network's ties
+- Added `from_ties()` to collect multiple networks into a multiplex network
+
+## Marking
+
+- Renamed `is.igraph()` to `is_igraph()` for igraph v2.0.0
+- Added `is_list()` for identifying a list of networks
+- Migrated `node_is_core()`, `node_is_cutpoint()`,  `node_is_fold()`, `node_is_isolate()`,  `node_is_mentor()` from `{migraph}`
+- Migrated `node_is_exposed()`, `node_is_infected()`, `node_is_latent()`, `node_is_recovered()` from `{migraph}`
+- Migrated `node_is_max()`, `node_is_min()`, `node_is_random()` from `{migraph}`
+- Migrated `tie_is_bridge()`, `tie_is_loop()`,  `tie_is_multiple()`, `tie_is_reciprocated()` from `{migraph}`
+- Added `tie_is_feedback()`
+- Migrated `tie_is_max()`, `tie_is_min()` from `{migraph}`
+- Added `tie_is_random()`
+
+## Mapping
+
+- Added `scale_edge_color_centres()`,  `scale_edge_color_ethz()`,  `scale_edge_color_iheid()`,  `scale_edge_color_rug()`,  `scale_edge_color_sdgs()`
+  - Fixed bug that meant edge scales were unavailable (closes #43)
+- `autographr()` now provides legends by default where multiple colours are used (closes #52)
+- `autographs()` now labels legends correctly for binary variables (closes #38)
+- `autographs()` now graphs just the first and last networks in a list (closes #45)
+- `autographs()` now includes an option whether the layout should be based on the first, last, or both of two networks (closes #48)
+
+## Data
+
+- Renamed `ison_konigsberg` to `ison_koenigsberg` and named the bridges
+- `ison_algebra` now in long multiplex format
+- `ison_karateka` now weighted, anonymous members are named by number, and "obc" variable renamed "allegiance"
+- `ison_lawfirm` enlarged from 36 to 71 nodes and now consists of three multiplex, directed networks
+- `ison_southern_women` names are now title case
+- Added `ison_hightech`, a multiplex, directed network from Krackhardt 1987
+- Added four `ison_monastery` datasets, three of which are signed and weighted, and the other is longitudinal, from Sampson 1969 (closes #49)
+- Added six `ison_potter` datasets in a list of networks, from Bossaert and Meidert 2013 (closes #47)
+- Added `ison_usstates` data on the contiguity of US states, from Meghanathan 2017
+
 # manynet 0.3.1
 
 2023-12-17