Release v1.2.3

Package

• Added {messydates} to Suggests
• Raised {manynet} floor to 2.3.1

Theming

• Added scale_x_mdate() and scale_y_mdate() (closes globalgov/messydates#104)
  • FUN resolves each messy date to one date; messydates::vmin by default
• Moved the colour checks into R/theme_aesthetics.R

Layouts

• Added check_crossings() for how many other ties each tie crosses
• Added check_slopes() for the slope each tie is drawn at
• Added check_lengths() for the total, max, and variance of tie lengths
• Added check_angles() for the angular resolution at each node
• Added check_drawing(), which reports those checks plus check_stress()

Tutorials

• Improved the isolate/bundling/backbone section ordering
• Each layout quality measure now names the function that measures it

Release v1.2.2

Package

• Shortened the startup message of .onAttach()

Graphing

• Improved how node_color= colours numeric node variables

Tests

• Fixed the arc strength test depending on the BLAS

Release v1.2.1

Layouts

• Fixed "valence" layout returning a poor layout for some random starts
  • The nodes now start on a circle, so one run resembles the next
  • The repulsion force between two close nodes is now bounded
  • Each step is now capped and cools over the iterations

Tests

• Fixed the tutorial test failing on a deprecation warning that the tutorial code does not raise itself
• Fixed the "valence" layout test depending on the random seed

Release v1.2.0

Package

• Removed the CRAN version check from .onAttach(), making library(autograph) faster to attach
  • Fixed .onAttach() not applying the ink of a persisted theme
• Added {goldfish} to Enhances
• Added {systemfonts} to Suggests
• Added a website-builds job to prchecks.yml, reporting whether the site builds
  • count_pages() was missing from the reference index, which stopped it
• Updated CONTRIBUTING with conventions for function names, NEWS.md bullets,
  the website reference index, and keeping tutorials and articles in step
• Added stocnet_completion() to offer values an argument accepts as RStudio completions
  • graphr(fict_lotr, node_color = Tab lists the node variables fict_lotr holds
  • Covers node and tie variables, layouts, label criteria, themes, and defaults such as isolates
  • Off unless asked for, since it replaces/encapsulates one of RStudio's internal functions; stocnet_completion(FALSE) restores it
  • A persist argument remembers the choice, as stocnet_theme() does
  • Values labelled with its class and its categories or range; a layout with the package that draws it

Layouts

• Improved layered layouts
  • Consolidated layered layouts onto one engine
    • "layered" is now default layout for directed acyclic networks
    • Deprecating "hierarchy" as "layered" is more consistent for two-mode networks
    • "lineage" is now exactly "layered" with the axes exchanged
    • Deprecating "alluvial" to free name for plot of changing membership composition
    • "railway" and "ladder" unchanged, but are alignment = "rungs"
    • Checks whether layout is appropriate for the network, and reverts to default if not
  • Minimises two costs: tie length (check_span()) and nodal offset (check_offset())
  • Added ranks= to choose the layers:
    • "compact" asks igraph::layout_with_sugiyama()
    • "generation" ranks each node by its distance from a root
    • "tight" (default) minimises total tie length while every tie points down at least one layer
    • a numeric node attribute lays the layers out by its values, spaced in proportion to them, which is what "lineage" used to take a rank for
  • Added alignment= to choose how a layer is spread out:
    • "straight" (default) draws ties as close to straight as ordering allows
    • "rungs" gives every layer same integer spacing
  • Each weakly connected component now laid out on its own and packed beside others
  • Fixed layout_layered() centring on a second mode node yet reading first mode labels
  • Fixed the direction of layers given as values to ranks=
  • Fixed layered layout labels to ignore label_repel
• Improved multilevel layout
  • Renamed "multilevel" layout to "levels" to avoid potential future collisions
  • Fixed layout_levels() to identify modes without having to name a level
  • Exposed method, alpha, beta, FUN1 and FUN2 arguments
• Deprecated "dyad", "triad", "tetrad", "pentad" and "hexad" layout names
  • "configuration" already picks the one matching the number of nodes
  • The layout_dyad() to layout_hexad() functions themselves are unchanged
• Fixed three broken paths in layout_concentric()
  • Fixed drawing each node of an unlabelled network on a circle of its own
  • Fixed erroring where a membership holds NA, now gathers NA nodes onto own circle
  • Fixed order.by=, which errored on every network; now orders nodes around each circle by that attribute, decreasing
• Fixed graphr(snap = TRUE) to use rotation and other improvements
• Added a "scaling" layout for multidimensional scaling
  • Scales classically up to a hundred nodes, and by pivots above that
  • Scales unweighted path distances, so it can handle signed/weighted networks
  • Lays each component out separately, where "pmds" refuses disconnected networks outright
  • Drawn with labelled axes at a fixed ratio, since these coordinates can be read
  • Captioned with check_stress() for Kruskal's stress-1, and console-reported where poor,
    as well as the share of distance variance two dimensions hold
• Added a "correspondence" layout for correspondence analysis
  • Places nodes by the similarity of their tie profiles
  • Reads directed networks symmetrically by default, but "out" or "in" possible
  • Refuses signed network, but double=TRUE an option
  • Console-reports low broomstick ratio dimensions and low cos2 nodes
• Added a layout_matching() alias so every layout has a short name
• Removed unreachable getNNvec()

Graphing

• Fixed graphr() clipping nodes at panel edges
  • Nodes were drawn at absolute sizes, but scales are expanded by a share of data range,
    so ggplot2's 5% left less room than the radius of a node in a small network
  • Room is now taken from node size, so small networks are given more space
• Added backbone= to graphr() for drawing dense, hairball "stress", "fr", "drl", "kk" networks
  • By default, networks with 50+ nodes and a mean degree ≥8 use backbones
  • TRUE/FALSE force, or specify filter/threshold (see manynet::tie_is_backbone())
• Improved graphr() to draw multilevel networks of interlocking one-mode and two-mode layers by default
  • Fixed tie opacity so that those between levels fade behind those within them
  • Fixed default node size in multilevel layout, which is now taken from how many nodes there are at each level rather than in the whole network
  • Fixed labelling to be plain text nudged away instead of white-boxed labels
• Fixed arcs drawn on layout that places two nodes at one point,
  e.g. graphr(ison_networkers, layout = "scaling")
• Fixed graphr() to draw parallel ties as a fan instead of one on top of another
• Fixed tie colouring in multiplex networks to color layers not signs by default
  • Signs are still drawn as linetypes
  • Added a legend for the tie linetype wherever it is the only thing showing the signs, and is titled by whatever color is showing
• Improved node shape legend to name modes where two-mode network records them instead of default "One" and "Two"
• Fixed size of self-loops to draw as a fraction of how far the layout spreads rather than at a fixed diameter of one coordinate unit
• Improved node_group to draw overlapping hulls (closes #51)
  • e.g. graphr(ison_adolescents, node_group = netrics::node_x_clique())
• Improved graphr() to note when a colour/shape legend grows past about 7 keys
• Fixed graphs() to collect guides even where panels held different ranges or categories (closes #15)

Theming

• Added persist= to stocnet_theme()
  • persist = TRUE writes it to tools::R_user_dir("autograph", "config")
  • Nothing written to disk unless passed explicitly
  • Setting a theme without it clears any choice persisted earlier
• Improved font detection in stocnet_theme() via {systemfonts}
  • Added list_fonts() for listing the font families R can see
• Added stocnet_medium() for standardising output to the expected medium:
  • "screen" (default), "presentation", "mobile", and "print"
  • ag_size() scales text, not node size or anything else
  • "print" draws on white irrespective of theme grounding
• Improved theme backgrounds to reach every plot, not only the graphs
  • Plot themes are now built with the ag_theme_*() wrappers
  • Blanked elements stay blank, so a graph keeps no axis text or coordinates
  • Ties, nodes, and labels with no colour take ag_ink() and the ground
• Added simulate_colorblind(), check_separation() and check_contrast() for checking palettes
  • Simulates deuteranopia, protanopia, and tritanopia (Machado et al. 2009)
  • Scores a pair by its worst case across those and normal vision
  • Added severity= to view anomalous trichromacy (deuteranomaly, protanomaly)
  • Added "grey" type to show a palette as print and photocopy may render it
• Added check_span() for scoring how far each tie travels down the page
• Added check_offset() for scoring how far each tie is from its ideal straight line
• Added ag_ink() for the colour a theme writes with
  • Used by axis text and reference lines, clearing 4.5:1 from the ground
  • Frees ag_base() to be light where that sets it off from the highlight
• Added ag_missing() for the neutral that data recedes into:
  • missing values, isolates, and any "other" remainder
• Improved ag_qualitative() to note when a palette is asked for more colours than it holds
• Improved every theme's categorical palette for colour-blind viewers
  • ag_qualitative() uses most distinct, own colors first not mixtures
  • Samples across the palette only where it holds too few colours
  • Kept "rainbow" in its own order, since fidelity to a spectrum is its point
• Improved some highlight pairs
  • Fixed "neon" highlight pair, a cyan and a green 12.7 apart
  • Fixed "ethz" and "cmu" highlight pairs by lightening their greys
• Fixed divergent palettes pairing a red pole with a green or teal one, such as in "ethz"
• Added a "clay" theme inspired by palette and fonts of Anthropic's Claude

Plotting

• Added plot.goldfishFit() for the four diagnostic panels a fit can supply
  • Deviance trace, Schoenfeld smooths, score processes, and waiting times
  • Draws only from what the fit stores, leaving a missing panel out
  • Draws the waiting-time panel for exact-time models only
  • Draws the compact term strings the test itself carries, which do not
    repeat where an effect appears over two networks
  • Reports how many terms the Schoenfeld panel dropped
  • Fixed the Schoenfeld panel to select terms by column position
    • The labels it matched on intersect the effect names on the intercept
      alone, so it drew one term where four were asked for
• Added plot.goldfishGOF() for each effect's cumulative score process
  • Draws the Brownian-bridge bands th...

Release v1.1.2

Merge pull request #58 from stocnet/develop

v1.1.2

Release v1.1.0

Merge pull request #56 from stocnet/develop

v1.1.0

Release v1.0.3

Merge pull request #55 from stocnet/develop

v1.0.3

Release v1.0.2

Merge pull request #54 from stocnet/develop

v1.0.2

Release v1.0.1

Merge pull request #53 from stocnet/develop

v1.0.1

Release v1.0.0

Merge pull request #42 from stocnet/develop

v1.0.0