# manynet 2.1.3

## Class

- Fixed stocnet validation test issue

## Describing

- Fixed `mode_names.stocnet()` and `layer_names.stocnet()` to look up correct info names

## Manipulating

- Improved `add_info()`
  - `add_info(.data)` (so no further arguments) now checks to see whether metadata may be added and prompts the user to add it if so
  - `add_info(.data, optional = TRUE)` extends this to further, optional metadata
  - This includes prompting the user by layer for multiplex networks

# manynet 2.1.2

## Package

- Updated title/description text
- Updated README
  - Updated TOC to include new wrangling section
  - Added package migration note to README
- Updated startup messages with migration notesand links to `{autograph}`, `{netrics}`, and `{migraph}`
- Removed a set of defunct wrappers for moved/retired functions

## Making

- Fixed reference formatting of DOI and citation text

## Coercion

- Improved `expect_nodes()`/`expect_ties()` and introduces internal active-context helpers
- Fixed `as_diffusion.igraph()` to derive diffusion events from changelists

## Manipulating

- Added `filter_ties.igraph()` and `filter_ties.stocnet()`
- Improved active context inference across `mutate_nodes.stocnet()`, `mutate_ties.stocnet()`, `filter_nodes.stocnet()`, and `filter_ties.stocnet()`
- Added `bind_changes.igraph()` and delegated 'tbl_graph' method to it

## Modifying

- Added `to_correlation.matrix()` S3 method

# manynet 2.1.1

## Package

- Updated README for CRAN submission

# manynet 2.1.0

## Package

- Updated exported registrations and reference documentation for expanded method coverage

## Coercion

- Added `as_globallist()` for extracting global variables from 'igraph' and 'stocnet' objects
- Added `as_stocnet.data.frame()` for coercing edgelists to stocnet objects (closes #138)
- Improved `make_stocnet()` construction, indexing, and validation of nodes, ties, changes, info, and globals
- Improved `as_stocnet()` coercion for `data.frame` and `tbl_graph` inputs
- Fixed #137 by extending time variable class validation to include integer and POSIXlt (thanks @auzaheta)
- Fixed #140 and #141 by making sure `make_stocnet()` aborts early and informatively when node labels do not match (thanks @auzaheta)

## Manipulating

- Added `add_tie_attribute()`
- Added `bind_nodes()` for adding nodes and ties from another network
- Added `arrange_changes()` and `arrange_nodes()` as generics for reordering nodes and ties in a network
- Added `gather_changes()` as a generic for gathering changes up to a time point
- Added `rename_changes()` for renaming change variables and `rename_globals()` for renaming global variables
  - Improved 'data.frame' and by extenion 'stocnet' `rename_*()` methods to rename variables when no arguments given
- Added `select_ties()`, `select_changes()`, and `select_globals()` for selecting variables
  - Improved 'data.frame' and by extenion 'stocnet' `select_*()` methods to reorder variables when no arguments given
- Added `filter_nodes()`, `filter_ties()`, and `filter_changes()` as generics for filtering nodes, ties, and changes in a network
- Added `summarise_ties()` for summarising tie variables
- Added `join_nodes.stocnet()` for joining a nodelist to a stocnet object
- Added 'stocnet' methods for `arrange_ties()`, `bind_ties()`, `mutate_nodes()`, `mutate_ties()`, and `rename_nodes()`
- Renamed `add_changes()` to `bind_changes.tbl_graph()`
  - Added `bind_changes.stocnet()` for binding on groups of changes to a stocnet object
- Improved `from_ties()` to accept named arguments instead of a named list, improving consistency with other modifying functions
  - Added `from_ties.stocnet()` for creating a multiplex stocnet object from more than one network, including handling of tie types as layers and carrying forward nodal attributes
- Improved node filtering and reindexing behaviour in `stocnet` objects so ties and changes remain aligned
- Improved all manipulating generics by adding .default methods that coerce to supported graph classes and then restore original classes, improving consistency across classes and reducing the need for users to coerce before manipulating

## Modifying

- Added `join_nodes()` for joining two nodelists
- Added new 'stocnet' methods for common modifications
- Added `mutate_globals()` for mutating global variables in a network
- Improved many `to_*()` default methods to coerce through supported graph classes and then restore original classes
- Improved conversion consistency across direction, projection, paths, plexity, correlation, and weight transformations
- Fixed default dispatch in scope and transformation helpers, including `to_subgraph()`

## Marking

- Added `is_cognitive()` for identifying cognitive social structure networks
- Added `is_egonet()` for identifying egocentric networks
- Improved `is_*()` handling across `stocnet`, `igraph`, and `tbl_graph` inputs
- Fixed several default `is_*()` methods to return logical values reliably after coercion
- Fixed `is_dynamic.stocnet()` to look for more time-type variables
- Fixed #135, which was due to faulty two-mode test (thanks @schochastics)

## Describing

- Added printing of the globals list for stocnet objects (closed #139)
- Improved `net_nodes()`, `net_node_attributes()`, and `net_tie_attributes()` coverage for table and network-like inputs
- Improved network metadata extraction defaults and naming behaviour across classes
- Fixed `net_nodes.stocnet()` and `net_dims.stocnet()` to work with unlabelled networks

# manynet 2.0.1

## Package

- Fixed checkmark printing issue

# manynet 2.0.0

## Package

- Changed to R 4.1 syntax including the native pipe (`|>`), the `{dplyr}` R dependence anyway
- Moved measuring, marking functions (node marks, tie marks, node selection, nodal diff marks), membership, and motif functions to `{netrics}`
- Moved `run_tute()`, `extract_tute()`, and tutorial 0 to `{migraph}`
- Moved tutorials 3–6 to `{netrics}`
- Removed `{autograph}`, `{learnr}`, and `{netdiffuseR}` from suggested dependencies
- Began using functional testing

## Making

- Renamed `create_ego()` to `collect_ego()` to better signal the different input structure expected
- Renamed `read_cran()` and `read_pkg()` to `collect_cran()` and `collect_pkg()` for consistency with other collecting functions
- Added directed parameters to `create_cycle()` and `create_wheel()` (undirected by default)
- Dropped `generate_permutation()` as no longer necessary
- Fixed `play_segregation()` to be less verbose
- Most common read/write methods now add file suffixes if passed filenames without them

## Coercion

- Added new `stocnet` class for representing multilevel, multiplex, multimodal, signed, dynamic, or longitudinal networks as a structured list of tibbles and metadata
  - Added `make_stocnet()` for straightforward construction of `stocnet` objects
  - Added `validate_stocnet()` for checking and suggesting improvements to `stocnet` structure
  - Added `as_stocnet.igraph()` for converting igraph objects to `stocnet`, including converting tie types to layers
  - Added `value` class to hold and print values of different classes held in a list vector
- Fixed `as_matrix.igraph()` for multiplex networks
- Fixed `as_matrix.network()` and `as_igraph.network()` bugs related to inheriting integer names
- Internalized `diffnet` coercion so that `{netdiffuseR}` is no longer required

## Manipulating

- Renamed `collect_changes()` to `gather_changes()`
- Improved `add_info()` so that if no further arguments are given it checks to see whether metadata may be added
  - Added `add_info.stocnet()` for adding metadata to `stocnet` objects
- Renamed `mutate_net()` to `mutate_info()` for consistency
- Renamed `net_info()` to `as_infolist()` for clarity
- Fixed #132 by adding a `network` method for `add_node_attribute()`
- Added stocnet methods for node and tie attribute extraction
- Fixed `join_nodes()` to work with unlabelled networks

## Modifying

- Fixed `to_ties.igraph()` for unlabelled networks
- Fixed `to_mode1()` and `to_mode2()` to work with unlabelled networks
- Fixed `to_no_missing()` rlang data pronoun issue
- Fixed `to_tree()` to use updated igraph function name
- Fixed `from_ties()` to be quieter when joining

## Describing

- Added `seq_nodes()` and `seq_ties()` for indexing network elements, exported for use in other packages
- Added `net_modes()` and `net_layers()` for describing network structure
- Added `net_nodes.matrix()` for extracting node count from matrix objects
- Made `net_node_attributes()` and `net_tie_attributes()` into generics with stocnet methods
- Renamed `net_node_names()` and `net_tie_names()` to `mode_names()` and `layer_names()` respectively for consistency with `net_modes()` and `net_layers()`
  - Fixed `mode_names()` and `layer_names()` to look for older grand-nested variable names where necessary
- Added stocnet methods for `net_nodes()`, `net_dims()`, `net_ties()`, `net_name()`, `mode_names()`, and `layer_names()`
- Added `network` method for `net_name()`

## Marking

- Fixed `is_egonet()` to return correct value (`FALSE`) for non-netlists
- Fixed `is_signed()` to no longer expect integers
- Added `diff_model` method for `is_changing()`
- `is_manynet()` now recognises the `stocnet` class
- Added `stocnet` methods for `is_labelled()`, `is_signed()`, `is_complex()`, `is_multiplex()`, `is_changing()`, `is_longitudinal()`, `is_dynamic()`, `is_twomode()`, and `is_directed()`

# manynet 1.7.2

## Making

- Fixed #126 with a `stopifnot(is.scalar(ties))` in `generate_citations()`
- Improved `generate_citations()` to be clear that it doesn't yet work on two-mode networks
- Improved `describe_network()` to include "network" as a suffix

## Modifying

- Added `net_attributes()` for returning the names of graph attributes
- Added `net_info()` for returning the list of graph attributes
- Improved `net_waves()` to now return waves = 1 for cross-sectional networks

## Marking

- Fixed `node_is_isolate()` to work with signed networks
- Fixed `node_is_pendant()` to work with signed networks

## Tutorials

- Fixed bug in "tutorial1" where `{renv}` was misinterpreting a hint as a package dependency

# manynet 1.7.1

## Package

- Restructured website
- Removed unnecessary global variables
- Exporting `expect_nodes()` and `expect_ties()` for use in other packages

## Making

- Added `net_name()` for obtaining network name if available
- Added `net_node_names()` and `net_tie_names()` for network element information
- Fixed `write_graphml()` to coerce to igraph first

## Modifying

- Improved `to_mode1()` and `to_mode2()` to carry forward nodal and tie attributes during projection
- Improved `to_mode1()` and `to_mode2()` to drop unnecessary nodal information
- Improved `to_uniplex()` to handle multimodal multiplex filtering correctly and retain tie type information
- Fixed #123 by inserting NAs before converting networkDynamic to igraph
- Fixed `add_changes()` to work with tbl_graph
- Fixed `filter_nodes()` to use `dplyr::all_of()`
- Added `interpolate()` helper for injecting missing data
- Restructured modifying function documentation around transformations (e.g. direction)

## Measuring

- Split `measure_attributes` documentation into separate nodes and ties pages

## Motifs

- Fixed `net_by_mixed()` to work with multiplex networks

## Data

- Compiled `ison_marvel_relationships` and `ison_marvel_teams` into single multiplex `fict_marvel` dataset

# manynet 1.7.0

## Making

- Improved vector printing to be more succinct and suggest `print_all()`
- Improved printing methods for changing mnet objects

## Modifying

- Added `delete_changes()` for deleting all changes from a changing network
- Improved `to_waves()` to work with networks that are changing, longitudinal, or both
- Fixed `as_diffusion()` to not trim off final wave in the report
- Fixed `as_diffusion()` to return correct E and R compartments for waning diffusion models

## Marking

- Improved `is_longitudinal()` to only check for tie waves and not nodal changes

## Measuring

- Improved `net_diversity()` and `node_diversity()`
  - No longer offers a cluster option, which can be obtained using `over_membership()`
  - Added more methods for calculating diversity, including Teachman's, coefficient of variation, and the Gini coefficient
  - Improved `net_diversity()` and `node_diversity()` to use and declare methods appropriate for the vector of attributes
- Added `net_homophily()` and `node_homophily()` for measuring homophily according to different methods including
  - Krackhardt's EI index of heterophily as well as its inverse as a measure of homophily
  - Yule's Q as a further measure of homophily
  - Geary's C as a measure of homophily for numeric attributes
- Updated documentation for richness, diversity, and homophily measures
- Fixed `node_is_latent()`, `node_is_infected()`, `node_is_recoverd()` to work with changing networks
- Improved `node_is_exposed()` to work with changing networks and now accepts a time argument
  
## Tutorials

- Fixed description of `to_directed()` and `to_redirected()` in the data tutorial

# manynet 1.6.7

## Making

- Fixed `generate_configuration()` methods since igraph >= v2.1.0 required

## Tutorials

- Added more glossary items for diversity tutorial

# manynet 1.6.6

## Modifying

- Fixed `generate_configuration()` to use recent versions of `igraph::sample_degseq()` correctly
- Added further testing

## Tutorials

- Fixed duplicate chunk label in data tutorial

# manynet 1.6.5

## Package

- Removed extracted tute scripts from root folder
- Added extensive testing for core and older functions

## Making

- Exported `describe_*()` functions for describing networks, nodes, ties, and changes

# manynet 1.6.4

## Making

- Added `read_gdf()` for importing GDF files
- Improved mnet object printing to publish the number of each type of tie in multiplex networks

## Modifying

- Fixed `join_nodes()` not recognising nodelists correctly

## Measuring

- Fixed #114 by updating net_heterophily documentation
- Added `node_randomwalk()` closeness centrality
- Added `node_subgraph()` centrality

## Tutorials

- Fixed bug where tutorials were not autoloading necessary packages
- Moved glossary to own script and added more tutorial 5-relevant entries
- Added more glossary keys to tutorial 5

## Data

- Improved `fict_actually` to be a multiplex network (thanks @korakotbua)

# manynet 1.6.3

## Tutorials

- Added more glossary items on centrality, modularity
- Excluded setup details when extracting a tutorial script
- Added French phrases to tutorials 3-6

# manynet 1.6.2

## Making

- Fixed #113 relating to igraph v2.2.0+ and explicit sample_bipartite functions
- Added `read_pkg()` for creating a network of the function interdependencies
within a package

## Modifying

- Added familiar $ operations for `mnet` objects
  - There is now dollar lookup functionality

## Measures

- Fixed bug in `node_coreness()` where data wasn't recognised within pipes

## Memberships

- Added `node_in_core()` for categorising nodes into 2+ core/periphery groups

## Motifs

- Added `net_by_hierarchy()` for characterising networks by their graph theoretic dimensions of hierarchy

## Data

- Added `ison_emotions`
- Renamed `irps_nuclear`
- Separated out data scripts into their different categories

## Tutorials

- Added `{autograph}` to setups for all manynet tutorials
- Improved data tutorial
  - Removed manynet two-mode question from data tutorial
  - Added more detail on examining data to data tutorial
- Improved topology tutorial
  - Using k-coreness in section on core-periphery
  - Added hierarchy multichoice
  - Demonstrated how to interpret hierarchy measure
  - Added more challenging comparison of hierarchy in two networks
  - Updated several glossary terms

# manynet 1.6.1

## Package

- Dropped mapping from function overview on website
- Dropped viz tutorial, moved to `{autograph}`
- Added CITATION
- Improved `run_tute()` and `extract_tute()` to search for `{autograph}`

## Printing

- Improved `describe_changes()` to work with time as well as begin/end tie attributes

## Making

- Added `create_windmill()`
- Added `create_wheel()`
- Added `create_cycle()`

## Modifying

- Fixed `to_uniplex()` test so that it doesn't rely on random sampling

## Marking

- Improved `is_multiplex()` to recognise more tie attributes

## Data

- Added `irps_nuclear_discourse` for goldfish and various testing of dynamic networks
- Added `ison_judo_moves` for judo move sequences

# manynet 1.6.0

## Package

- Dropped viz-related dependencies: `{ggplot2}`, `{ggraph}`, `{patchwork}`, 
`{ggdendro}`, `{concaveman}`, `{gifski}`, `{graphlayouts}`, `{ggforce}`,
and `{BiocManager}`

## Classes

- Added mdate pillar shaft for pretty printing of NAs in messydate variables

## Modifying

- Improved `to_no_missing()` to record missing removal
- Improved `to_no_isolates()` to record isolate removal
- Improved `to_giant()` to record giant component scoping
- Improved `to_matching()` to record matching
- Fixed `to_matching()` triggering warnings from handling NAs (thanks @schochastics for fixing #109)
- Improved `to_mentoring()` to record mentoring
- Improved `to_eulerian()` to record Eulerian pathing

## Measuring

- Improved `net_core()` with method options for calculating correlation, distance, ndiff, and diff

## Membership

- Improved `node_coreness()` to implement Borgatti and Everett's continuous coreness algorithm
- Moved previous functionality of `node_coreness()` to `node_kcoreness()`

## Mapping

- Moved `graphr()`, `graphs()`, and `grapht()` to `{autograph}`
- Moved palette functionality to `{autograph}`
- Moved remaining layouts to `{autograph}`
- Moved theme functionality to `{autograph}`
- Dropped remaining plot functions
- Dropped or avoided using `{autograph}`-related functions in examples to
make package lighter
- Please see `{autograph}` for continued development of these features

# manynet 1.5.1

## Package

- Removed failing URLs

## Modifying

- Improved `to_mode1()` and `to_mode2()` to record projection change

# manynet 1.5.0

## Package

- Updated pandoc setup in pushrelease workflow

## Making

- Dropped print and summary methods for diffs_model (moved to `{migraph}`)

## Modifying

- Added `to_no_missing()` for removing nodes with missing data
- Fixed `as_diffusion.mnet()` so that it includes "diff_model" class

## Measuring

- Dropped plotting methods (moved to `{autograph}`)
- Added Page 2010 citation to `node_richness()` documentation

## Memberships

- Fixed `node_in_leiden()` to use resolution parameter in call to igraph

## Data

- Improved `table_data()` so that it lists components, longitudinal, dynamic, 
and changing data
- Added more description for `fict_lotr`
- Added `irps_revere` data

# manynet 1.4.1

## Making

- Added Deffuant model to `play_learning()`
- Added fatality parameter to `play_diffusion()` for e.g. SID models
- Improvements to `create_ego()`
  - Now accepts an explicit ego in the call, e.g. create_ego("Andy")
  - Now uses pluralization to prompt alter?s
  - Can now create two-mode ego networks
  - Uses new `snet_prompt()` for easier to read consoles 
  - Uses new `snet_minor_info()` for reminding users to assign the function
  - Now names ego in the title of the resulting object
  - Fixed bug where ego duplicated if already in the roster
  
## Modifying

- Extended `to_matching()` to work on the more general class of stable matching
problems, including where nodes have different capacities

## Marking

- Added `node_is_universal()`

## Measuring

- Improved node measure printing with a spark bar

# 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 `snap`ped 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_graph`s
  - `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()`
