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v1.0.0#69

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jhollway merged 242 commits intomainstocnet/manynet:mainfrom developstocnet/manynet:developCopy head branch name to clipboardJul 8, 2024

Commits

Commits on Apr 30, 2024

• Updated manynet logo with stocnet address and colorsafe colorway

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Commits on May 2, 2024

• Added node_is_independent() for identifying nodes in largest independent sets

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• mark_nodes functions now infer network context

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Commits on May 10, 2024

• Added ison_greys dataset

  

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• Fixed bug in diffusion tutorial because minMSE not being declared

  

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• Version bump and NEWS

  

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Commits on May 23, 2024

• Updated ison_friends to be explicitly longitudinal

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• Fixed bug in create_core() where the membership inferred when passing an existing network was incorrect

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• is_multiplex() now excludes reserved tie attribute names other than type

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• Updated data documentation with revised multiplex definition

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• Restructured graphr, graphs, and grapht code

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• Updated NEWS

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Commits on May 24, 2024

• Drop guides/legends for node size and shape where there is no variation

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• Reexported ggplot2::scale_size()

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• Better legend title where there is variation in node_size

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• Added internal node size rescaling step, but wip

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• Added {minMSE} to decsription since it is now explicitly imported in documentation

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• Renamed logo files to avoid test issues

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• Commented out tests related to node attributes to avoid issues, for now

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• Fixed issues with tests for scales and themes

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• Better scaling for node size

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• Updated NEWS

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• Added more git explanation

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• Added population data to ison_usstates

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Commits on May 25, 2024

• Some further community documentation changes

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Commits on Jun 4, 2024

• Added more informative mesgaes for when users might have mispelled variable names

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• Added tests for variable names check in autographr()

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Commits on Jun 5, 2024

• Updated "concentric" layout to create layout even if some names are empty

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• Updated "concentric" layout to construct layout even when node names are missing

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• Added tests for new changes in concentric layout

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• Fixed issues with default "hierarchy" layout for two mode networks

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• Added tests for "hierarchy" layout for two mode networks

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• Updated NEWS for new changes

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• Updated NEWS for new changes

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• Added more tests for node mark functions

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• Fixed issues with additional tests for node marks

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Commits on Jun 6, 2024

• Added additional tests to tie mark functions

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Commits on Jun 13, 2024

• Added descriptions to tutorials

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Commits on Jun 14, 2024

• Added to_correlation()

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• Fixed documentation in to_correlation()

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• Added diffnet methods for as_igraph(), as_network(), and as_tidygraph()

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• Added diff_model methods for as_igraph() and as_matrix()

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• Added as_diffnet.diff_model() to coerce diff_model results into diffnet objects

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• Added as_diff_model.diffnet() to coerce diffnet objects into diff_model

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Commits on Jun 15, 2024

• Added as_diff_model() to coercion table/figure

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Commits on Jun 17, 2024

• Fixed as_diffnet documentation

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• Added to_correlation() tests

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• Added an explicit contact argument to play_diffusion, which can be used to control the basis of exposure

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• diffusion tutorial now uses graph*() instead of autograph*()

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• pkg_data() renamed to table_data(), the former now defunct, split into own documentation

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• Trimmed package size by dropping old logos

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• Added top/bot/3/5 helpers for testing

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• Migrated class_measures from migraph

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• Changed properties from mapping to measuring, functions now make_network_measure

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• Changed attributes from mapping to measuring, renamed node_mode() to node_is_mode() since it always returns a logical vector the length of the order of the network

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• Filled in NAMESPACE, added globalVariable for .data

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• Migrated closure measures from migraph

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• Migrated heterogeneity measures from migraph

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• Migrated hierarchy measures from migraph

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• Migrated holes measures from migraph

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• Migrated cohesion measures from migraph

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• Migrated diffusion measures from migraph

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• Migrated all centrality measures over from migraph

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• Migrated centrality tutorial from migraph

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• graphr() is now the default, autographr() has been deprecated

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• Renamed autographs() to graphs()

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• Renamed autographd() to grapht()

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• Updated pkgdown to includes measures, graph*

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• #major bump as manynet gains measures, grows more mature

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Commits on Jun 18, 2024

• Used node_is_mode() now within functions

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• Fixed documentation

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• updated function names in visualisation and centrality tutorials

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• re-rendered html files for centrality and visualisation tutorials

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• Documentation should use graphr()

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• Making sure make_node_measure() uses manynet::node_is_mode()

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• Fixing globalVariables issue

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• More renaming to graphr()

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• Since network_nodes() now returns a network_measure class object, tests need to unclass

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• Using c() to remove classing

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• c() to strip network_nodes of class

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• Updated tests for measure holes' functions

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• Using manynet functions in play_diffusion() where available

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• Fixed non-autograph test errors

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• Fixed autographr-related test issues

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• Fixed issue with node_closeness() to avoid {rlang} warnings

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• Added generate_configuration() for generating configuration models including for two-mode networks, note that for dense two-mode networks like ison_southern_women this can take a long time (many re…

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• Found a faster way of creating two-mode configuration models

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• node_exposure() now works with two-mode networks, which means play_diffusion does too

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Commits on Jun 19, 2024

• node_exposure() now only follows outgoing ties, making play_diffusion() work for directed networks

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• More helpful documentation for table_data()

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• node_exposure() now works on signed networks, which means play_diffusion() does too

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• Added is_attributed() to check for non-name/type nodal attributes

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• Migrated network_change() and network_stability() from migraph

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• table_data() now reserves enough room for the name of the dataset when printing, includes a column for the logical of whether the network includes attributes

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• node_attribute() and tie_attribute() return measures when the output is numeric

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• Updated as_ documentation

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• Added prevalence argument to play_diffusion() so that endogenous global prevalence can affect diffusion

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Commits on Jun 20, 2024

• Added class_members

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• Added class motifs

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• Migrated census measures from migraph, *_census() now renamed *_by_*(), renamed network_by_*() to net_by_*()

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• Fixed bug in as_diff_model where events were out of order and named instead of indexed

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• Removed explicit reflexive dependence

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• Exporting to namespace

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• More changes to diffusion tutorial

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• Fixed message bug in graphs()

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• Retaining network_measure and network_motif classes

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• Migrated over_*() from migraph

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• network_*() centrality measures renamed to net_*()

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• Updated centrality tests and tutorial

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• Renamed network_*() properties functions to net_*()

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• Renamed network_*() hierarchy measures with net_*()

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• Renamed network_*() heterogeneity measures with net_*()

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• Renamed network_*() closure measures with net_*()

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• Migrated k-selection functions from migraph

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• Migrated cluster methods from migraph

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• Migrated node_in_roulette() from migraph

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• Migrated equivalence functions from migraph

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• Migrated component partitioning from migraph

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• Migrated test_*() functions from migraph

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• Migrated node*core* functions from migraph

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• Renamed network_*() diffusion measures to net_*()

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• Renamed network_*() cohesion measures net_*()

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• Migrated feature measures from migraph

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• Migrated node_in_adopter() from migraph

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• Migrated community memberships from migraph

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• Updated internals of many functions to use new net_*() syntax

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• Diffusion tutorial updated with new net_*() syntax

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• Reverted to network_test class to retain backwards compatibility

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• Ensured all census functions are now _by_

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• Dropped rlang dependency

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• Fixed make_net_measure bug

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• Fixed various test issues related to net_measure

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• Dropped read_graphml testing to save space (nassau.graphml was 7.8MB+!)

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• Added remaining tutorials

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• Updated NEWS file

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• Removed duplicated functions in measure diffusion

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• Updated documentation

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• Minor edits to diffusion tutorial

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• Merge branch 'develop' of https://github.com/stocnet/manynet into develop

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• Updated pkgdown

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• Merge branch 'develop' of https://github.com/stocnet/manynet into develop

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• Migrate measures of network change from migraph

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• Fixed dependency bugs by adding some more suggests

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• Fixed some explicit dependence bugs

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• removed unnecessary legend code for graphs and corrected references to autographr and autographd

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• Converted node_in_core() to node_is_core()

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• Fixed various documentation issues

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Commits on Jun 21, 2024

• Rationalised member_/motif_ documentation

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• node_in_core() renamed to node_is_core() because it is now a mark

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• network_ changed to net_ in pkgdown

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• Fixed doc bug in member_diffusion, censuses now called motifs throughout

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• Added node_by_exposure() function to tabulate exposure across time

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• Added renamed network_*() functions to defunct list.

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• Fixed ordering issues with node_is_infected(), node_is_recovered(), and node_is_exposed()

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• Updated NEWS and documentation for new changes with node_marks

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• Added new tests for node marks

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• Using colorsafe colors in diffusion plots and graphs

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• Merge branch 'develop' of https://github.com/stocnet/manynet into develop

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• Now that measures are in manynet, can use the main node_adoption_time() in graphr()

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• Added previous versions of node_by_*(), net_by_*(), and node_in_*() functions to defunct list.

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• Merge branch 'develop' of https://github.com/stocnet/manynet into develop

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• Trimming manynet explicit from various internal function calls

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• Merge branch 'develop' of https://github.com/stocnet/manynet into develop

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• Corrected some doc

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• plot.diff_model() now allows users to trim how many simulated steps are shown to only those leading up to complete infection

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• Remigrated tests to migraph to keep things consistent

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• Added net_complete_infection() to measure how long a diffusion process takes to complete, moved diffusion members to same script as diffusion measures

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• Added %||% in case it is of utility

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• Fixed node_adoption_time() bug in graphr()

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• Using magrittr pipe consistently to ensure backwards compatibility

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• Fixed node_is/in_core() bug

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• Dropped %||% for now

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• Inverted when graphr() complains about variable spelling

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• Closed #51 with larger nodes

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• play_diffusion() now accepts nodal attribute names for thresholds

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• Some more doc on thresholds

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• Trimmed all the setup start from the diffusion tutorial

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• Rewrote influence cascades section to hold new hands more and added fun task

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• Rewrote linear thresholds section, including also a fun exercise with an 'empirical' network at the end

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• Smaller diff tute and doc updates

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Commits on Jun 22, 2024

• plot.diff_model() now uses prettier breaks on the x-axis, and the all argument works also for incomplete infections

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• Renamed plot.diff_model argument to all_steps so that it is more obvious what it does

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• play_diffusion() now accepts node names as seeds

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• Consolidated diffusion coercion into single as_diffusion() generic

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• Fixed bug in diffnet coercion where s included those already infected

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• Made it easier to use diffusion metrics on diffnet objects directly by including coercion

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• Renamed net_infection_length() to net_recovery() to avoid misunderstandings

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• Added net_total_infection() to measure the proportion/number of nodes that are infected by the end of the diffusion process

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• Fixed as_diffusion generic inconsistency

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• Corrected documentation to net_recovery()

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• Corrected as_diffusion documentation

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• events needed to be explicit

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• Fixed issue with net_hazard() return

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Commits on Jun 23, 2024

• Consolidated net_infection_*() functions together in own documentation

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• Added net_infection_peak() to identify when peak infection occurs in a diffusion

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• Updated CRAN comments to explain the situation with migraph

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• Added tests from migraph

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• Corrected smeg_diff doc

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• is_longitudinal() now recognises longitudinal networks in lists

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• make_diff_model now more careful with lists of networks

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• Updated pkg date

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• Added list methods for is_twomode(), is_labelled(), and is_complex()

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• node_infection_length() renamed to node_recovery()

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• net_nodes() now knows what to do with lists of networks

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• net_infection_total() now sums infections, not the amount that remain infected at the end of the process

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• node_thresholds() handles unlabelled networks better

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• First half of diffusion tute has more informative titles

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• More discussion on seeding to diffusion tute

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• Added check marks to the intro

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• net_recovery now censors by default, this is a placeholder until a lin estimator or similar

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• Updates to play_diffusion and graphr to make them netlist compatible

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• Fixed some chunk setup woes, and added LOTR free play box

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• Fixed chunk setup woes in back half of tute

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• Updated DeGroot section

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• Added eigenvector freeplay section on networkers

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• Added independent sets and other strategies section, added prevalence section

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• Added R0 section

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• Added herd immunity section

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• Added freeplay on greys

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• Updated html

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Commits on Jun 24, 2024

• Updated how node_is_recovered() works to allow for node to be susceptible again after recovery

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• Updated NEWS for latest changes

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• Updated NEWS file

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• Attempt to fix issues with node_exposure() for two mode networks

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• Attempt to fix node_exposure() issue for two mode networks

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• Returned tests to manynet for integrated workshop

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• Final doc changes before workshop

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• Updated node_exposure() function to work with two mode data

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Commits on Jul 1, 2024

• Updated ison_southern_women with women's surnames and titles, event/tie dates, and fixed bug with four extra ties

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• Added arrange_ties() to help with data manipulation

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Commits on Jul 4, 2024

• to_named() now draws an alphabetic sequence of names to assist pedagogy

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• Added some U and Q names to the baby_names internal data

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Commits on Jul 8, 2024

• is_multiplex() now ignores "date", "begin", "end" tie variables, ison_southern_women updated accordingly

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• Fixed bug in node_by_quad() where it wouldn't work for multiplex networks

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• Fixed bug in join_ties() so that it treats non-numeric tie variables correctly

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• Fixed rlang bug in to_named()

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• Updated test results for ison_southern_women

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• Dropped unnecessary :::

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• Moved tests back over to migraph

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• Updated NEWS

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• Updated README with measures, motifs, and members

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• Dropped konect link from make_read because link is unreliable

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