v1.0.0

[jhollway]

Description

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}

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_diffuson() 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 Fix inconsistencies with how diffusion models are plotted with graphs() and grapht() #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 Improve node sizing algorithm in graphr() #51)
• Fixed issues with "hierarchy" layout for two mode network (closes Hierarchy layout for two mode network does not work as expected (sometimes) #61)
• Updated "concentric" layout to accept unlabeled nodes (closes Fix concentric layout so that node names can be removed to improve visualisations  #68)

Modifying

• Fixed bug in as_diff_model() where events were out of order and named
• Added to_correlation() that implements pairwise correlation on network
• Added arrange_ties() for {dplyr}-like reordering of ties based on some attribute
• 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

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

Members

• Migrated members from {migraph}
  • Cliques memberships includes node_in_roulette()
  • Community and hierarchical memberships includes node_in_optimal(), node_in_partition(),
    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()
  • 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.

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.

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()

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

Checklist:

• PR form
  • Description above itemizes changes under subtitles, e.g. "## Data""
  • Any closed, fixed, or related issues are referenced and explained in the description above, e.g. "Fixed #0 by adding A"
  • Package builds on my OS without issues
• PR checks all pass for latest commit
  • CodeFactor check: Package improves or maintains good style
  • Package builds on Mac
  • Package builds on Windows
  • Package builds on Linux
  • CodeCov check: Package improves or maintains good test coverage
• Documentation
  • Any new or modified functions or data have roxygen style documentation in their .R scripts
  • Longer functions are commented inline or broken down into helper functions so that it is easier to debug in the future
  • PR description above and the NEWS.md file are aligned
  • DESCRIPTION file version is bumped by the appropriate increment (major, minor, patch)

[jaeltan]

new logo looks good to me, only the grey colour for the M makes the logo look a bit faded.

[jhollway]

The idea here was for the logo to mimic the grey used in default graphr() calls. But perhaps we should also reconsider that default choice?

[henriquesposito]

Thank you for all the work @jhollway !