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

Fixed bug in to_waves() where result was unordered

Mapping

graphr() now uses categorical palettes (effectively closing #60)

manynet 1.3.2

Measuring

Added net_correlation() for calculating the product-moment correlation between networks
Improved speed of make_network_measure by retrieving single call at parent level

manynet 1.3.1

Package

Fixed miscellaneous documentation issues, re roxygen
Separated out the data sections in pkgdown

Modifying

Added to_simplex.data.frame() and to_simplex.network()

Marking

Fixed bug in is_aperiodic() where it would not work in tutorial chunks

Measuring

Added over_membership() for obtaining summary statistics by a membership vector

Practicing

Fixed data pointers in several tutorials
Added glossary items to diffusion tutorial

manynet 1.3.0

Package

Improved user information in the console
- manynet cli functions now inherit parent frame
- Added manynet cli functions for success and progress along, seq, and nodes
Improved testing architecture
- Moving to nested testthats
- Added custom testthat function for expecting values and ignoring dimension names

Making

Added some names to created networks (create_ego(), create_empty(), create_filled(), create_ring(), create_star(), create_lattice())

Modifying

Fixed how as_matrix() handles signed networks
Added as_nodelist() for extracting nodelists from networks into tibbles
Added to_cosine()
Dropped to_galois() until it can be refactored
Split reformatting documentation into format, reformat, and deformat groups of functions
- Added to_signed() for adding signs to networks
- Added to_weighted() for adding weights to networks

Mapping

Fixed default color ordering so that red is the highlight
Fixed bug in graphr() where line types were inferred incorrectly
Improved graphr() so that layouts can now be snapped to a grid, mileage may vary
Improved theme handling so that it is set globally (WIP)
- Added highlight themes
- Added background themes
- Added categorical themes
Improved configurational layouts
- Added dyad, pentad, and hexad layouts to configurational layouts
- Renamed quad layout to tetrad layout

Marking

Added node_is_pendant() for identifying pendant nodes
Added node_is_neighbor() for identifying adjacent nodes
Added tie_is_imbalanced() for identifying ties in imbalanced configurations

Measuring

Added summary.network_measure() to return z-scores and p-values for measures
Added node_vitality() for measuring closeness vitality centrality
Fixed #98 by dropping scale and normalization for node_eigenvector()

Memberships

Improved community detection options for new users
- Community detection algorithms now reformat networks as necessary or suggest that it be used on only the giant component
- Added node_in_community() which runs through most salient community detection algorithms to find and return the one with the highest modularity
- Updated documentation on resolution parameters
Improved node_in_regular() to inform user which census is being used
Renamed node_by_quad() to node_by_tetrad() to be more consistent with Greek origins
- Restored and updated documentation about the various configurations
Added summary.network_motif() which returns the z-scores for the motif scores based on random or configurational networks, traces progress
Fixed bug in plot.network_motif() where motif names were not identified correctly, internal make_network_motif now inherits call information

Modelling

Added cluster_cosine() for another equivalence option
Added internal documentation for depth_first_recursive_search

Practicing

Improved how run_tute() fuzzy matched so that insertions are not as costly
Improved tutorials with glossary architecture
- Added gloss(), clear_glossary(), and print_glossary() for adding glossaries to tutorials
Updated tutorials
- Updated community, position, and topology tutorials with glossaries, free play sections, and gifs
- Fixed miscellaneous issues in these tutorials
- Added faction section to community tutorial

Data

Added irps_wwi, a dynamic, signed network
Renamed ison_blogs to irps_blogs, added info
Renamed ison_books to irps_books, added info
Renamed ison_usstates to irps_usgeo, added info
Renamed ison_friends to fict_friends, added info and fixed directed issue
Renamed ison_greys to fict_greys, added info
Renamed ison_lotr to fict_lotr, added info
Renamed ison_thrones to fict_thrones, added info and some additional nodal attributes
Renamed ison_potter to fict_potter, added info and combined waves into single object

manynet 1.2.6

Package

Fixed errors when testing without {concaveman}
Fixed errors when plotting some examples without {ggdendro}

manynet 1.2.5

Package

Fixed errors when testing on extended features and Suggested packages not available

manynet 1.2.4

Package

Fixed thisRequires() bug by testing for interactivity
Dropped brokerage census examples

Modifying

Improved to_ego() and to_egos() to specify direction

manynet 1.2.3

Mapping

Fixed bug in graphr() where user not informed about {concaveman} dependency
Fixed graphr() examples

manynet 1.2.2

Package

Updated all tutorials with different themes to make them more distinctive
Updated centrality tutorial with gifs
Updated visualisation tutorial with a few extras

Modifying

Added to_dominating() for extracting the dominating tree of a given network

Mapping

Reworked graphr() to make function more concise and consistent (thanks @henriquesposito)
- This allows new functionality and improves debugging moving forward

Measuring

Updated closeness centrality documentation
Improved node_eccentricity() to allow normalisation, appear in closeness documentation
Added node_stress() as a new betweenness-like centrality measure
Added node_leverage() as a new degree-like centrality measure

manynet 1.2.1

Making

All read_*() now print the command used to the console if the (default) file.choose() is used
Added read_gml()
Updated references, structure, and DOIs to make and modify documentation

Measures

Updated references, structure, and DOIs to centrality, diffusion, and other measures, as well as to marks, motifs, memberships, and models
Added more documentation on node_power()

Data

Added ison_dolphins
Added ison_books
Added ison_blogs

manynet 1.2.0

Package

Added progress updates, information, and unavailability errors to several functions
- These can be silenced by setting options(manynet_verbosity ="quiet")
- Where a feature is unavailable, users are directed to the Github issues page
Added console theme to color the startup and various warning or info messages

Making

Added create_ego() for collecting ego networks through interviews, including arguments for:
- Indicating whether a roster should be used, otherwise follows a name generator approach
- Indicating whether nodes should be interpreted, i.e. nodal attributes collected
- Indicating whether ties between alters should be requested
Added create_motifs() for creating networks that correspond to the isomorphic subgraphs of certain size and format

Modifying

Improved print.mnet()
- Prints multiplex types if available
- Prints both nodesets for two-mode networks
Added add_info() for adding grand info to tidygraph objects
- This includes the name of the network, node sets and ties, DOI, year and mode of collection
Fixed to_unweighted() so that it passes through unweighted networks correctly

Mapping

Added set_manynet_theme() to set theme (re #60), but not yet fully implemented

Marking

Improved is_multiplex() to ignore "name" tie attributes

Measuring

Added node_authority() and node_hub() centrality measures
Added node_equivalency() for calculating four-cycle closure by node
Extended net_equivalency() to one-mode networks

Members

Fixed node_in_equivalence() to use census directly

Motifs

Added plot methods for network_motif and node_motif classes that use create_motifs()
Added node_by_dyad() for node level dyad census
Added net_by_quad() for network level quad census
Fixed node_by_quad() to avoid {oaqc} dependency (#89), more flexible but slower
Fixed print.node_motif() to convert to tibble and add modes and names where available only upon print
- The underlying object is still a matrix, used for equivalence and blockmodelling

Data

Updated ison_southern_women with grand info
Updated ison_laterals with reordered nodes

manynet 1.1.0

Package

Added beautiful message on startup
- Depends on {cli}
- Reports version number
- Offers different suggestions each time it is loaded
- Can be silenced using suppressPackageStartupMessages()
Improved error warnings, stop() replaced by cli::cli_abort()
Improved website structure
- Structured make_, manip_, map_, mark_, measure_, and model_ documentation
- Improved function overview layout for measures
Updated Github Actions scripts
- Updated renaming and releasing binaries (thanks @auzaheta)
- Using actions/download-artifact@v4 to address dependabot security warning
- Using actions/upload-artifact@v4
Removed {minMSE} dependency
Moved {roxygen2} dependency to Config/Needs/build
Dropped unnecessary {grDevices} and {png} dependencies
Dropped unnecessary {network} reexports
Using globalVariables
Improved run_tute() and extract_tute() to look for installed packages and report progress

Making

Added read_cran() for creating networks of package dependencies on CRAN
- Gathers dependency graph for whole CRAN by default, but can also trace successive outgoing dependencies from a single package (speed increase depends on the package, but is nearly 9x faster for {manynet})
- Also gathers nodal information about whether compilation is required
Added generate_man() for generating dyad census conditional uniform graphs
Fixed #86 by making sure igraph::sample_islands in generate_islands() only takes a single integer and not a vector

Manipulating

Improved as_tidygraph() to add an additional class 'mnet' that is used for prettier printing
- Uses make_mnet() (internally) for future-proofing
- print.tbl_graph() renamed to print.mnet()
- print.mnet() uses 'grand' data if available
Improved bind_ties() to be more flexible about the input it accepts, converting all input into the required edgelist
Added to_ego() for obtaining a single neighbourhood
Added tbl_graph and network methods for delete_nodes() and delete_ties()
Added examples for add_ties() and delete_ties() in documentation
Fixed bug in to_unnamed.igraph() when used with already unlabelled networks

Marking

tie_marks are now named vectors
- Printing vectors no longer requires unique names
Added tie_is_path() for tracing the ties on a particular path
Added tie_is_triplet() for returning all the ties that are members of transitive triplets
Added tie_is_forbidden() for identifying ties in forbidden triads
Improved tie_is_transitive() efficiency, now only retrieves the edgelist once
Improved is_aperiodic() to remove {minMSE} dependency and offer a progress bar if it takes longer than 2 seconds
Fixed bug in tie_is_triangular() to do with altpath naming

Measuring

tie_measures are now named vectors
Added node_distance() for measuring the distance from or to particular nodes
Fixed #84 related to how node_degree() processed isolates in calculating strength in weighted networks

Data

Updated all ison_ data with new as_tidygraph()
Added 'grand' data to ison_adolescents as a test
Added ison_thrones on kinship arcs between Game of Thrones characters, with 'grand' data
Consolidated ison_monastery_ data into ison_monks, a single multiplex, signed, weighted, longitudinal network

manynet 1.0.5

Making

Added create_degree() for creating networks of a given degree sequence, including k-regular graphs
Added generate_citations() for citation models
Added generate_fire() for forest-fire models
Added generate_islands() for island models
create_explicit() now has its own documentation

Marking

Added tie_is_triangular() for identifying ties in triangles
Added tie_is_cyclical() for identifying ties in cycles
Added tie_is_transitive() for identifying ties involved in transitive closure
Added tie_is_simmelian() for identifying Simmelian ties

Manipulating

generate_permutation() renamed to to_permuted()

Mapping

Updated how graphr() plots edges in directed networks
Removed automatic legends for signed networks
Fixed other legends issues

Data

table_data() can now report on data from multiple packages
- {manynet} and {migraph} are included by default, and if any are not installed they are just ignored
table_data() can now filter by any reported formats, such as 'directed' or 'twomode'

Website

Added more structure to Modifying section
Added more structure to Mapping section

manynet 1.0.4

Modifying

as_matrix.igraph() now only draws from the "weight" attribute and not, e.g. "type"
Fixed bug in to_blocks() related to categorical membership variables

Marks

Tie marks now infer networks when used within e.g. mutate_ties()

Memberships

node_names() now returns names of the form "N01" etc for unlabelled networks
Fixed how plot.matrix() works for unlabelled networks
Added more on density in community tutorial

Mapping

British spelling arguments now appear further back in e.g. graphr()
Fixed how graphs() recognises ego networks so it is compatible with other splits

manynet 1.0.3

Mapping

Fixed #73 "node_color" mapping issue with graphr()
Fixed issues with variable name warnings in graphr()
Fixed #76 numeric "node_size" issues with graphr() function
Closed #66 so graphs() automatically uses "star" layout to plot ego networks
Fixed #41 so arguments for graphr(), graphs(), and grapht() also accept British spellings

Memberships

Fixed bugs in hierarchical community detection algorithms for unconnected networks

manynet 1.0.2

Package

Added alttext to images in the README, tutorials, and website
Added CRAN link to homepage
Updated favicons
Added more structure to the function overview

Making

Updated intro tutorial with images, exercises, questions, and more explanation and structure
Updated data tutorial with images, new function names, questions, and more explanation and structure
Updated data tutorial with more details on adding and deleting nodes, ties, and attributes
Updated topology tutorial with new function names and more structure

Mapping

Updated viz tutorial with examples of graphs() and grapht()
Updated viz tutorial with more details and examples on colors and theming
Updated viz tutorial with overview, examples, and details on layouts, including force-directed, layered, circular, spectral, and grid layouts

Measures

Updated centrality tutorial with images, new function names, and more structure
Updated centrality tutorial with more interpretation of centrality measures
Updated position tutorial with new function names and more structure

Memberships

Updated community tutorial with new function names and more structure

manynet 1.0.1

Package

Test of to_subgraphs() no longer sampled

manynet 1.0.0

Package

Updated {manynet} logo with stocnet GitHub address and color blind safe colorway
Fixed bug in diffusion tutorial because of undeclared {minMse} dependency
Renamed all functions starting with the network_* prefix to net_* for conciseness
Migrated network measures, membership, motifs, and models' functions from {migraph}
Migrated community, position, topology, and diffusion tutorials from {migraph}
Added descriptions to tutorials

Making

Fixed bug in create_core() where the membership inferred when passing an existing network was incorrect
Added generate_configuration() for generating configuration models (including for two-mode networks)
play_diffusion() now includes an explicit contact argument to control the basis of exposure

Marking

node_is_*() functions now infer network data context
Added node_is_independent() for identifying nodes among largest independent sets
is_multiplex() now excludes reserved tie attribute names other than type, such as "weight", "sign", or "wave"
Added is_attributed() to check for non-name nodal attributes
Fixed issues with ordering in node_is_latent(), node_is_recovered(), and node_is_infected() (closes #71)
Added list methods for is_twomode(), is_labelled(), and is_complex()

Mapping

Renamed functions to graph networks graphr(), graphs(), and grapht() (autographr(), autographs(), and autographd() are now deprecated)
node_size now an aesthetic, allowing scale_size(range = c(...,...)) to be used
Reexported scale_size() from {ggplot2}
graphr() now rescales node size depending on network size (closes #51)
Fixed issues with "hierarchy" layout for two mode network (closes #61)
Updated "concentric" layout to accept unlabeled nodes (closes #68)

Modifying

to_named() now randomly generates and adds an alphabetic sequence of names, where previously this was just a random sample, which may assist pedagogical use
- baby_names (internal) now includes a few extra "Q" and "U" names
Added to_correlation() that implements pairwise correlation on network
Added arrange_ties() for {dplyr}-like reordering of ties based on some attribute
Added to_correlation() for calculating the Pearson correlation
- This takes a method argument for "all", "diag", "recip", or "complex"
- These are similar to functions implemented by Ron Breiger and shared by him in correspondence
Fixed bug in as_diff_model() where events were out of order and named

Marking

is_multiplex() now recognises "date", "begin", and "end" as reserved

Measuring

Migrated measures from {migraph}
- Centrality measures
  - Degree-related centrality measures include node_degree(), node_deg(), node_indegree(), node_outdegree(), node_multidegree(), node_posneg(), tie_degree(), net_degree(), net_indegree(), and net_outdegree()
  - Betweenness-related centrality measures include node_betweenness(), node_induced(), node_flow(), tie_betweenness(), and net_betweenness()
  - Closeness-related centrality measures include node_closeness(), node_reach(), node_harmonic(), node_information(), tie_closeness(), net_closeness(), net_reach(), and net_harmonic()
  - Eigenvector-related centrality measures include node_eigenvector(), node_power(), node_alpha(), node_pagerank(), tie_eigenvector(), and net_eigenvector()
- Closure measures include net_reciprocity(), node_reciprocity(), net_transitivity(), node_transitivity(), net_equivalency(), and net_congruency()
- Cohesion measures include net_density(), net_components(), net_cohesion(),
  net_adhesion(), net_diameter(), net_length(), and net_independence()
- Diffusion measures include net_transmissibility(), net_recovery(), net_reproduction(), net_immunity(), net_hazard(), net_infection_complete(), net_infection_total(), net_infection_peak(), node_adoption_time(), node_thresholds(), node_recovery(), and node_exposure()
- Heterogeneity measures include net_richness(), node_richness(), net_diversity(), node_diversity(), net_heterophily(), node_heterophily(), net_assortativity(), and net_spatial()
- Hierarchy measures include net_reciprocity(), net_connectedness(), net_efficiency(), and net_upperbound()
- Holes' measures include node_bridges(), node_redundancy(), node_effsize(),
  node_efficiency(), node_constraint(), node_hierarchy(), node_eccentricity(), node_neighbours_degree(), and tie_cohesion()
- Features' measures include net_core(), net_richclub(), net_factions(), node_partition(), net_modularity(), net_smallworld(), net_scalefree(), net_balance(), net_change(), and net_stability()
Updated properties from mapping to measuring
Updated attributes from mapping to measuring
- Renamed node_mode() (deprecated) to node_is_mode() since it returns a logical vector
- Updated node_attribute() and tie_attribute() to return measures when the output is numeric
Updated node_exposure() to work with two-mode and signed networks
Fixed node_constraint() to work with weighted two-mode networks, thanks to Toshitaka Izumi for spotting this
All measure functions can now be used in e.g. mutate() without specifying .data
Added net_independence() for calculating the number of nodes in the largest independent set
node_coreness() now returns 'node_measure' output
node_exposure() now sums tie weights where passed a weighted network

Members

Migrated members from {migraph}
- Cliques memberships node_in_roulette() (previously node_roulette())
- Community and hierarchical memberships includes node_in_optimal(), node_in_partition() (previously node_kernaghinlin()), node_in_infomap(), node_in_spinglass(), node_in_fluid(), node_in_louvain(), node_in_leiden(), node_in_betweenness(), node_in_greedy(), node_in_eigen(), and node_in_walktrap()
- Components' memberships include node_in_component(), node_in_weak(), and node_in_strong() (NB: node_in_component() is no longer phrased in the plural)
- Core-periphery memberships include node_is_core() and node_coreness()
- Diffusion memberships include node_in_adopter()
- Equivalence memberships include node_in_equivalence(), node_in_structural(), node_in_regular(), and node_in_automorphic()
- Note that these functions were previously named node_*(), but including the preposition _in_ is more consistent.
node_member class is now categorical
- make_node_member() now converts numeric results to LETTER character results
- print.node_member() now works with categorical membership vectors
- print.node_member() now declares how many groups before reporting the vectors
All membership functions can now be used in e.g. mutate() without specifying .data
Hierarchical clustering algorithms now return dendrograms

Motifs

Migrated motifs to take census of network, node positions, and brokerage from {migraph}, these include node_by_tie(), node_by_triad(), node_by_quad(), node_by_path(), net_by_dyad(), net_by_triad(), net_by_mixed(), node_by_brokerage(), net_by_brokerage()
- Note that these functions were previously named *_*_census(), but the preposition _by_ is more consistent.
node_tie_census() now works on longitudinal network data
Fixed bug where print.node_motif() wasn't printing the requested number of lines

Methods

Migrated methods from {migraph}
- Methods for equivalence clustering include cluster_hierarchical() and cluster_concor()
- Methods for selecting clusters include k_strict(), k_elbow(), and k_silhouette()
Several improvements to cluster_concor()
- cluster_concor() now uses to_correlation() for initial correlation
- It still uses stats::cor() for subsequent iterations
- Fixed how cluster_concor() handles unlabelled networks
- Fixed how cluster_concor() handles two-mode networks
- Fixed bug where cluster_concor() cutoff resulted in unsplit groups
cluster_hierarchical() now also uses to_correlation()

Data

Added ison_greys dataset, including some corrections to that published in {networkdata}
Updated ison_friends dataset to be explicitly longitudinal
Updated ison_usstates dataset with population data (Alaska and Hawaii missing)
Updated ison_southern_women dataset with surnames, titles, event dates, and corrected ties
Updated data documentation with revised multiplex definition

manynet 0.4.4

2024-03-15

Modifying

Fixed documentation issue with to_scope() for CRAN resubmission

manynet 0.4.3

2024-03-13

Mapping

Fixed issues with autographr() examples that were taking too long to run
Separated documentation for autographr(), autographs(), and autographd() functions
Closed #64 by adding aliases for autographr(), autographs(), and autographd() functions
Closed #65 by fixing bugs with how node_is_infected(), node_is_recovery(), node_is_latent() work for network lists

manynet 0.4.2

2024-03-12

Making

Closed #57 by updating play_diffusions() to revert future plan on exit
Fixed bug with how generate_random() works for two-mode networks with specified number of ties

Mapping

Closed #6 by updating how "lineage" layout works and places nodes on Y axis
Closed #39 by making autographr() more flexible and efficient in setting variables to aesthetics
Updated themes to be compatible with newer and older versions of {ggplot2}
Added "configuration" layout for small triad/quad networks

Modifying

Updated to_reciprocated.matrix() to consistently work with matrices

manynet 0.4.1

2023-12-24

Package

Fixed minor documentation bug in run_tute()
pkgdown urls now point to "stocnet/manynet"
Closes #34 by pushing changes to CRAN

manynet 0.4.0

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
Updated tests to be consistent with future {ggplot2} release

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

Making

as_tidygraph.diff_model() no longer creates names for unlabelled networks

Modifying

to_waves.diff_model() now adds three logical vectors as variables, "Infected", "Exposed", and "Recovered"
- Relies on parallels to migraph's node_is_latent(), node_is_infected(), and node_is_recovered()
- Fixed bug in wave naming

Mapping

autographr() now shapes seed, adopter, and non-adopter nodes using a parallel to migraph's node_adoption_time() for
- Improved guide/legend labelling and positioning
autographs() now colors susceptible, exposed, infected, and recovered nodes correctly
autographd() now colors susceptible, exposed, infected, and recovered nodes correctly

manynet 0.3.0

2023-12-15

Package

Overhaul of the README to summarise many of the unique aspects of the package (closed #36)

Making

Added as_tidygraph() method for diff_model objects
Added as_siena() method for tidygraph objects

Modifying

Manipulating functions now called Modifying
to_waves() now works on diff_model objects, add attributes and names
is_multiplex() now recognises a tie/edge 'type' attribute as evidence of multiplexity
Deleted unnecessary reexports from other packages
- igraph::is_bipartite() is superseded by is_twomode()
- tidygraph::activate() is superseded by mutate_ties() and similar functions
Fixed bug by replacing older igraph::as_incidence_matrix() and igraph::graph_from_incidence_matrix() with igraph::as_biadjacency_matrix() and igraph::graph_from_biadjacency_matrix()

Mapping

autographr() now plots diff_model objects, showing the diffusion as a heatmap on the vertices
autographs() and autographd() now utilise network information in diff_model objects to provide better layouts (closed #17)
Fixed bug with specifying node_size in autographd()
many_palettes replaces iheid_palette
Added new palettes, themes and scales for graphs (closed #9)
- theme_ethz(), scale_color_ethz()/scale_colour_ethz(), and scale_fill_ethz() for ETH Zürich
- theme_uzh(), scale_color_uzh()/scale_colour_uzh(), and scale_fill_uzh() for Uni Zürich
- theme_rug(), scale_color_rug()/scale_colour_rug(), and scale_fill_rug() for Uni Gröningen

Data

Added ison_physicians data that includes four, multiplex networks with adoption data

manynet 0.2.10

2023-12-06

Package

Fixed documentation issues with run_tute()

Making

Added read_graphml() and write_graphml() for importing and exporting graphml objects, mostly wrappers for igraph functions.

Mapping

autographd() and autographs() can now be used for plotting diffusion models.
- Updates to to_waves() and autographd() to account for 'exposed' nodes in diffusion models.
Updates to layouts
- Updates to hierarchical layout so that node name can be specified for centering the layout
- Updated theme_heid() layout

Data

Added faction attribute to ison_starwars data, thanks to coding by Yichen Shen and Tiphaine Aeby

manynet 0.2.9

2023-11-15

Package

Updated run_tute()function to "fuzzy" match tutorial names

Mapping

Added +.ggplot() method for visualising multiple plots in the same pane
Added custom theme theme_iheid for plots
Added custom scale_ family of functions for changing colour scales in plots
Updated autographr():
- Added "center" option for hierarchy layout that places events or actors in the middle alike "bip" and "bip3" layouts
- Added "lineage" layout that fixes node positions according to values in y axis
Fixed bugs with autographd() function

manynet 0.2.8

2023-11-02

Package

Fixed tutorials documentation issue for CRAN

manynet 0.2.7

2023-11-01

Making

Updated treatment of adjacency matrices in as_igraph() in accordance with upcoming updates to {igraph} package (closing #27)

Manipulating

Added to_mentoring function

Mapping

Fixed bugs in autographr() related to edge_size and edge_color
Fixed bugs and updated label placements for "circular" and "concentric" layouts for autographr()
Fixed issues with self-ties in autographr()
Updated tests for autographr()

Data

Added ison_friends, a one-mode network on character connections of a popular TV series

manynet 0.2.6

2023-10-25

Package

Added documentation for tutorial helper functions

Making

generate examples leverage autographr() again

Manipulating

Fixed bug in to_redirected.tbl_graph()
print.tbl_graph() no longer mentions the object class

Mapping

layout_tbl_graph_concentric() now works with two-mode networks, multiple levels for one-mode networks, and accepts new vectors
Added layout_tbl_graph_multilevel() for laying out multilevel networks
Added layout_tbl_graph_triad() and layout_tbl_graph_quad() configurational layouts

Data

Added ison_starwars, a collection of seven weighted interaction networks on a popular film franchise
ison_networkers names are now in title case, not all caps

manynet 0.2.5

2023-10-19

Package

Added 'tutorial0' for those less comfortable with R
Added run_tute() helper for quicker access to {manynet} and {migraph} tutorials
Added extract_tute() for extracting the main code examples from {manynet} and {migraph} tutorials
Added purl = FALSE to tutorial chunks that are not needed for extraction (thanks @JaelTan)
Updated website with new functions run_tute() and extract_tute()

Mapping

Fixed remaining issues with node_group and updated documentation

manynet 0.2.4

2023-10-11

Package

README now includes Macports installation instructions
Added {graphlayouts}, {ggforce}, and {multiplex} to Suggested

Manipulating

Added to_galois() for transforming networks into partially ordered Galois lattices

Mapping

Fixed bug in node_shape argument in autographr()
Fixed bug in node_group argument in autographr(), closes #11
Fixed bug in inconsistent default colour scheme for node_color and node_group in autographr()
autographr() now automatically bends arcs for reciprocated ties when directed network is not too large/dense
autographr() now accepts unquoted variables as arguments
autographr() now uses graphlayouts::layout_igraph_multilevel where appropriate
Default node labelling now larger and further from nodes in circular layout

Data

ison_algebra now an anonymised network (again)

manynet 0.2.3

2023-09-17

Package

Fixed URL in read_

manynet 0.2.2

2023-09-17

Package

README now points to {migraph} earlier

Tutorials

Fixed various bugs in first (data) tutorial

Map

Fixed explicit node_shape bug

Data

Added ison_lawfirm data from Lazega, see documentation for more details
Upgraded ison_marvel data to latest igraph specification

manynet 0.2.1

2023-08-11

Map

Fixed documentation issues with map_palettes

manynet 0.2.0

2023-08-11

Package

Closed #4 by adding thisRequiresBio() helper function to download Bioconductor packages
Upgraded ison data to latest igraph specification
- Added ison_konigsberg for illustrating Seven Bridges of Konigsberg
- Removed ison_brandes2 and added potential modal type as extra variable to ison_brandes
- Consolidated ison_bb, ison_bm, ison_mb, and ison_mm into a list of networks called ison_laterals

Make

Added create_explicit() for creating networks based on explicit nodes and ties

Manip

Added delete_nodes() for deleting specific nodes
Added to_eulerian() function that returns a Eulerian path network, if available, from a given network

Map

Moved additional is_ functions from {migraph}
- Added is_connected() to test if network is strongly connected
- Added is_perfect_matching() to test if there is a matching for every node in the network
- Added is_eulerian() to test whether there is a Eulerian path for a network
- Added is_acyclic to test whether network is a directed acyclic graph
- Added is_aperiodic to test whether network is aperiodic
Added partition layouts
- Added layout_tbl_graph_alluvial() that places successive layers horizontally
- Added layout_tbl_graph_concentric()that places a "hierarchy" layout around a circle
- Added layout_tbl_graph_hierarchy() that layers the nodes along the top and bottom sequenced to minimise overlap
- Added layout_tbl_graph_ladder()that aligns nodes across successive layers horizontally
- Added layout_tbl_graph_railway that aligns nodes across successive layers vertically
Added theme_iheid() function that themes graphs with colors based on the Geneva Graduate Institute

manynet 0.1.2

2023-06-20

Package

Added tutorials for package
- Moved and updated "data" tutorial from {migraph}
- Moved and updated "visualisations" tutorial from {migraph}

manynet 0.1.1

2023-06-09

Package

Removed commented out examples
Added more detail on what various functions return

Manipulates

Added na_to_mean.data.frame()

Maps

Added network_dims.network()

manynet 0.1.0

2023-06-07

Package

Split up the {migraph} package, adding the Make, Manipulate, and Map functions to this package
Added package documentation
- Added .github files
- Added README structured around the problems the package solves
Improved consistency and readability
- Functions that take data as their first argument has that first argument named .data
- Added new print.tbl_graph method that offers easy to interpret information
- Note that this method is exported but not currently documented
Reduced package dependencies considerably
- Many are now weak dependencies; a dialog is invoked when the calling function is used for the first time and the user is prompted to install the missing package
Added extensive testing
Added new 'manynet' logo

Makes

Added read_*() functions, e.g. read_edgelist()
Added write_*() functions, e.g. write_edgelist()
- Added write_matrix() for exporting to matrices
Added create_*() functions, e.g. create_lattice()
- All create_*() functions return tbl_graph class objects
Added generate_*() functions, e.g. generate_smallworld()
Added ison_* network data, e.g. ison_southern_women

Manipulates

Added as_*() functions, e.g. as_igraph()
- Fixed as_edgelist.network()
- Fixed as_network.data.frame()
- Fixed as_network.tbl_graph()
Added join_*() functions, e.g. join_ties()
Added add_*() functions, e.g. add_node_attribute()
- All create_*() functions return tbl_graph class objects
Added mutate_*() functions, e.g. mutate_ties()
- With mutate_ties(), it is no longer necessary to activate(edges)
Added rename_*() functions, e.g. rename_ties()
Added is_*() functions, e.g. is_dynamic()
- Fixed is_labelled() to work correctly with multiple network formats
Added to_*() functions, e.g. to_mode1()
- This includes functions for reformatting, transforming, and splitting
- This also includes functions for returning networks with missing data replaced by some imputed values
- Fixed to_giant.network()
- to_directed() now a method
- to_subgraphs() now returns a list of tbl_graphs
- to_reciprocated() now works on edgelists, matrices, tbl_graphs, and networks
- to_acylic() now works on matrices, tbl_graphs, and networks
Added from_*() functions, e.g. from_egos()
- Fixed from_subgraphs()
Added "grab" functions, e.g. network_nodes()
- network_dims() is now a method

Maps

Added autographr(), autographs(), and autographd()
Added layout functions
- Fixed layout_tbl_graph_concentric()

Files

NEWS.md

Latest commit

History

NEWS.md

File metadata and controls

manynet 1.4.0

Making

Modifying

Marking

Measuring

Motifs

Data

Learning

manynet 1.3.3

Modifying

Mapping

manynet 1.3.2

Measuring

manynet 1.3.1

Package

Modifying

Marking

Measuring

Practicing

manynet 1.3.0

Package

Making

Modifying

Mapping

Marking

Measuring

Memberships

Modelling

Practicing

Data

manynet 1.2.6

Package

manynet 1.2.5

Package

manynet 1.2.4

Package

Modifying

manynet 1.2.3

Mapping

manynet 1.2.2

Package

Modifying

Mapping

Measuring

manynet 1.2.1

Making

Measures

Data

manynet 1.2.0

Package

Making

Modifying

Mapping

Marking

Measuring

Members

Motifs

Data

manynet 1.1.0

Package

Making

Manipulating

Marking

Measuring

Data

manynet 1.0.5

Making

Marking

Manipulating

Mapping

Data

Website

manynet 1.0.4

Modifying