autograph 1.2.1

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

autograph 1.2.0

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 the effect’s p-value was read from
  • Draws x on the object’s own process time, named for the clock it records
  • Inverts the distribution the event-clock p-value comes from
• Added plot.goldfishTimeTest() for the scaled Schoenfeld residuals
  • Draws a smooth per effect, with the fitted estimate as the reference
  • Colours the scatter by period under method = "periods"
• Added plot.goldfishOnset() for the parameter path and information accrual
  • Windows both panels on the excursion, so each coefficient gets its scales
  • Draws the proportional diagonal, the departure from which is the finding
  • Added view = c("both", "path", "accrual") to select a single panel
• Added plot.goldfishMargins() for observed against expected activity
  • Draws martingale residuals where the model class defines a compensator
  • Draws the calibration ratio where it does not, from the recorded scales
  • Draws the top actors furthest from the reference, and counts the rest
  • Draws level against shape where goldfish supplies dispersion
  • Names both omissions: under two completed spans, and beyond top
• Added a page argument to plot() on the per-term diagnostics
  • Applies to goldfishGOF, goldfishTimeTest, and goldfishOnset
  • Added count_pages(), reporting the count without rendering
  • Renamed from ag_pages(), since ag_ is for the theme accessors
  • Errors with the page count where page is past the last
  • Leaves each figure as it was where page is omitted
• Renamed the goldfish classes to a package prefix and a camelCase noun
  • goldfishOutliers, goldfishChangepoints, goldfishOnset, goldfishMargins, goldfishGOF, goldfishTimeTest, goldfishScoreTest, and goldfishFit
  • A name such as test_gof is what a sibling package would pick too, and two packages emitting one class string cannot be told apart by dispatch
  • Renamed the dispatch methods and the precooked fixtures to match
  • Kept the older class names as aliases, so such objects plot as before
  • Documented the convention in CONTRIBUTING, for the whole ecosystem
• Improved plot.goldfishOutliers() and plot.goldfishChangepoints()
  • Renamed from plot.outliers.goldfish() and plot.changepoints.goldfish()
  • Read the metadata each object carries rather than inferring it
  • Plot the .series column, so a diagnostic called with effect = is drawn as that term’s series rather than as a log-likelihood trace
  • Fixed both to facet on process, so no line crosses a process boundary
  • Fixed plot.goldfishChangepoints() to draw each process’s own breaks
  • Fixed plot.goldfishOutliers() to read the now-logical outlier column
  • Rewrote plot.goldfishChangepoints() for the tibble with a cpt column
    • Labels the axis with break times only where they are numbers, so a dated event stream keeps its date scale
• Added precooked goldfish_margins, goldfish_gof, goldfish_time, and goldfish_onset, and refreshed the two older fixtures
  • Each is stamped with the goldfish version that produced it, 1.9.21
  • goldfish_outliers comes from a receiver-choice model of the calls
  • The others come from event models of the fisheries_treaties layer
• Replaced cli::cli_abort() in gf_facet_paged() with snet_abort()
• Replaced em dashes in R/plot_diagnostics.R since only ASCII is portable
• Fixed signed branch of plot.matrix() hard-coding its poles

Tutorials

• Moved the decorative gifs in the visualisation tutorial into quiz answer feedback

autograph 1.1.2

Package

• Improved the declared dependencies
  • Removed {knitr} from Suggests: it was used solely by the tutorial tests, which now extract the tutorials’ {r} chunks with the same small scanner used in {manynet} and {netrics} (verified to yield an identical expression set to knitr::purl() on the autograph tutorial)
  • Removed {tidygraph} from Imports: its only functional use was reading the edgelist’s target column in .infer_end_cap(), which now uses igraph::as_edgelist() (verified to give identical end caps)
  • Promoted {graphlayouts} from Suggests to Imports, since it is required for grapht()’s default “stress” layout (without it, wave-to-wave node transitions silently degraded to a static aggregate layout) and is installed regardless as {ggraph} imports it; its requireNamespace()/thisRequires() guards have been removed
  • Declared a minimum {manynet} version (>= 2.2.1)
• Updated the GitHub Actions workflows
  • Updated the actions to their latest major versions (actions/checkout@v7, actions/upload-artifact@v7, actions/download-artifact@v8), replacing some long-outdated @v2 pins
  • Updated the website deploy job’s r-lib/actions/setup-pandoc from @v1 to @v2, matching every other r-lib/actions step
  • Added checks that metadata and tutorial vignettes correspond
• Improved the test suite while reducing what CRAN has to run
  • The functional audits now fail rather than skip when AUTOGRAPH_STRICT_AUDIT=true, which the CI check step now sets, so a broken layout or plot method can no longer pass CI green
  • Fixed the layout audit’s fixture and argument maps, which paired several layouts with networks they cannot lay out; because skip() aborts the enclosing test_that(), the first such mismatch had been silently preventing every later layout from being audited at all (the layout audit goes from 21 to 108 assertions)
  • Coverage is now measured with NOT_CRAN=true, without which every skip_on_cran() test — most of the suite — was skipped while covr ran, badly under-reporting coverage
  • release and pkgdown no longer run under if: always(), so a failing R CMD check can no longer tag a release or deploy the website
  • Replaced graphr()’s sweep over every bundled {manynet} dataset with a representative sample, and dropped the plot.* smoke tests now subsumed by the plot-method audit; CRAN-visible test time falls while CRAN-visible assertions rise
  • Added an edge-case audit (test-functional_errors.R), an audit of the user-facing layout_* aliases, and examples for the ag_* palette accessors and configurational layouts, none of which were previously covered
  • Theme-mutating tests now restore the previous theme with on.exit(), so global theme state cannot leak between parallel test workers
• Updated the website and README
  • Updated favicons
  • Split Graphing from Plotting functions
  • Updated README to send visualisation examples to the website
  • Fixed README double logoing on pkgdown build, and added alttext
• Updated CONTRIBUTING with the package architecture, conventions, and dev commands
• Updated remaining base R stop(), warning() and stopifnot() calls to the {manynet} cli interface

Graphing

• Improved graphr()’s labels argument to label a selection of the nodes, where previously the only alternative to labelling every node was labelling none
  • labels now also accepts a depth of ranks (labels = 5), a measure to rank by (labels = "betweenness", or labels = c(betweenness = 5) for both), the name of a logical node attribute, or a logical/name/position vector of the nodes to label
  • Selection is by rank rather than by headcount, so nodes tied at the cut are labelled together, using netrics::node_is_max(); a two-mode or multilevel network is ranked within each mode or level, so a dense level cannot crowd the others out of the labelling
  • Networks of more than 30 nodes now label only their most central nodes by default, reporting how many; labels = TRUE still labels every node. manynet::fict_marvel went from 194 overlapping labels to 10
  • Labels are drawn from the selected rows rather than by blanking the rest, so no space is reserved (and nothing is repelled away from) labels that are not drawn
  • grapht() resolves the selection once across all waves, so the same nodes stay labelled from frame to frame, and graphs() resolves it once for all its panels; grapht()’s own default above 30 nodes remains no labels at all
  • {netrics} is only suggested, so an automatic selection falls back to a random sample when it is not installed, and a measure asked for by name says what to install
• Fixed graphs()/grapht() erroring (“Can’t combine ..1 and ..2 ”) on a longitudinal network whose changing node attributes are stored as non-character vectors (e.g. the logical active flag and numeric height/mass in fict_starwars)
  • Such networks now split into waves via a guarded to_waves() that coerces the offending attributes when {manynet}’s splitter cannot combine them
• Fixed graphr(..., snap = TRUE) erroring (“‘-’ only defined for equally-sized data frames”) whenever a node sat exactly on a grid point
  • depth_first_recursive_search() compared each node against a distance vector that still included its own zero self-distance, so an exact hit selected that entry and yielded an empty grid point; the self-distance is now dropped before the nearest vacant point is chosen
  • two-mode networks hit this on their very first node, since their coordinates are exactly 0 or 1
• Improved graphr() to ignore snap = TRUE for layered layouts (“hierarchy”, “railway”, “ladder”, “alluvial”, “multilevel”, “lineage”, “layered”)
  • These layouts encode rank, mode, or generation along an axis, which square-grid snapping would collapse
• Fixed graphr() erroring with “argument "node_color" is missing, with no default” when passed a list of networks; the call is now forwarded to graphs() as written, rather than argument by argument
• Improved how graphr() checks the attribute names given to its aesthetic arguments
  • A mistyped node or tie attribute name now errors immediately, naming the argument and offering the closest match: graphr(net, node_color = "welth") reported “Unknown colour name: welth” at draw time, and now reports that “welth” was not found among the node attributes and asks whether “wealth” was meant
  • The same applies to node_shape (previously “Shape aesthetic contains invalid value”), node_size and edge_size (previously “Aesthetics must be either length 1 or the same as the data (8)”), node_group, and edge_color
• Improved the error when the input is not a network, which now names the argument and the class given, rather than reporting a missing method for as_tidygraph()
• Fixed isolates being validated only when the network happened to contain isolates, so the same typo errored on one network and was ignored on another
• Fixed node_size values between 0 and 1 being silently multiplied by ten; node_size = 0.5 now means 0.5, while a vector of proportions is still rescaled to stay visible
• Fixed graphs() producing empty panels by checking waves against the number of networks available
• Added a set of internal argument checks (R/graph_checks.R) shared by graphr(), graphs(), grapht(), the layout_*() functions, and stocnet_theme()
  • An unrecognised value now errors immediately, naming the argument and offering the closest match, rather than falling through to {ggplot2}, {grid}, or match.arg() (so isolates = "drop" reports isolates, rather than “‘arg’ should be one of …”)
  • A value that differs only in capitalisation is now used as intended, with a note, instead of being rejected: node_color = "Wealth" finds the wealth attribute
  • Note that these checks are stricter than before: a mistyped attribute name used to be ignored silently or to fail later, and now stops the call
• Updated group-reduction note in graphr() and constant-colour note shared by graphr() and grapht() so that their wording cannot drift

Plotting

• Improved plot.node_member() to draw its dendrogram with {ggraph}
  • Passes hclust object’s own merge heights to the dendrogram layout to reproduce the previous plot’s leaf order, merge heights, cluster label colours, and cutpoint line
  • Branches now drawn in ag_base() rather than black, matching the height axis and so respecting the active stocnet_theme()
  • Removed {ggdendro} from Imports
• Updated a stale doc cross-reference in plot.node_member(), which pointed at manynet::node_in_community(); that function moved to {netrics} in manynet 2.0.0
• Updated terse or dead-end messages to say what to do next, including plot.node_motif()/plot.network_motif() (“Cannot plot these motifs yet, sorry.”), match_color(), plot.diff_model(), and the concentric and hierarchy layouts (“Duplicated nodes in layers!”)
• Updated zero-variance note shared by three GOF plot methods so that their wording cannot drift

Layouts

• Improved the error on an unrecognised layout, which now names the argument, suggests the nearest layout, and lists autograph’s own layouts, rather than reporting “object ‘layout_tbl_graph_stresss’ not found”
  • Passing a layout function (e.g. layout = igraph::layout_with_fr), rather than its name, now says so instead of erroring with “invalid indexing”
• Added checks of the membership/level/rank arguments that the partition layouts require, which name the argument and offer the closest match

Theming

• Improved stocnet_theme() to error with the nearest match on an unrecognised theme name, instead of warning and silently leaving the previous theme in place; giving more than one theme name is also caught

Tutorials

• Added a colour blindness section to the visualisation tutorial
  • Covers simulate_colorblind(), check_separation(), and how palettes are ordered
  • Notes that the “rainbow” theme is not a colour-blind safe scheme
• Added a note on installing a theme’s fonts to the visualisation tutorial
• Updated the README with the case for colour-blind readable palettes
• Updated visualization tutorial to use colour/color consistently
• Updated the Labels section of the visualisation tutorial to cover selecting which nodes to label, replacing the mutate(name = ifelse(...)) workaround it used to recommend
  • fict_lotr, the tutorial’s running example, has 36 nodes, so its graphs now name only its most central characters; the surrounding prose says so and shows how to choose otherwise
  • Regenerated vignettes/articles/visualising-networks.Rmd and the pre-rendered tutorial HTML to match

autograph 1.1.1

Graphing

• Fixed grapht() example, which took too long to run, by couching it in \donttest{}
• Improved graphs() to accept bare longitudinal or dynamic networks
  • Splits it into waves or time slices automatically (consistent with grapht()), instead of erroring with “invalid to use names()<- on an S4 object of class ‘dgCMatrix’”
• Fixed various errors and warnings in graphr()/graphs() on signed, directed, or changing networks:
  • Fixed recycling warnings (“longer object length is not a multiple of shorter object length”) in graphr() on a complex network
    • arc geom’s strength parameter now excludes loop edges, which are drawn separately by geom_edge_loop0()
  • Fixed spurious warning (“no non-missing arguments to max; returning -Inf”) in graphr() on a changing network without any adoption events (e.g. fict_potter)
    • such networks now rendered as standard changing networks rather than routed through the diffusion node-colour mapping
  • Fixed fails at draw time with “invalid hex digit in ‘color’ or ‘lty’” in graphr() on a signed multiplex network (e.g. fict_marvel)
    • ties on non-signed layers (which have a missing sign) are now drawn solid/positive rather than passing NA to grid
  • Fixed error with “Aesthetics must be either length 1 or the same as the data” in graphr()/graphs() on signed longitudinal or directed networks (e.g. to_waves(ison_monks))
    • per-tie sign linetypes are now mapped through aes() (with an identity scale) so ggraph’s edge geoms expand and subset them consistently with edge colour and width
  • Fixed graphr(..., snap = TRUE) erroring on two-mode networks: their default “hierarchy” layout is now left un-snapped (with an informative message) since collapsing its layered coordinates onto a square grid is not meaningful, while snapping a two-mode network under a force-directed layout continues to work; also hardened the grid-snapping search so a coordinate landing exactly on a grid point is no longer mistaken for a node’s zero self-distance

Tutorials

• Updated visualisation tutorial with a bit more structuring of further options

autograph 1.1.0

Package

• Test coverage raised by introducing functional testing infrastructure (tests/testthat/helper-functional.R and test-functional_*.R) for:
  • the layout family
  • the plot.* S3 method family
  • the ag_* palette accessors across all themes
  • graphr()’s aesthetic arguments each enumerated automatically and audited against fixture grids
• Removed the unused internal helper seq_nodes()
• Excluded the interactive-only palette helper ggpizza() from coverage
• Added {migraph} to Suggests (used in tests only)

Graphing

• Improved how graphr() treats labels
  • Fixed labels overlapping nodes (closes #13): labels now keep clear of node borders automatically by giving ggrepel each node’s true rendered size, with label_dist adding a further points-based gap (mirroring igraph’s vertex.label.dist) and label_repel = FALSE selecting a fixed offset instead of repulsion.
  • This also fixed a pre-existing bug where non-repelled labels rendered with a fully transparent fill under this package’s theme, making them invisible over nodes.
• Improved grapht() has been rewritten for smoother, more consistent animations of dynamic networks
  • Node positions now transition seamlessly between waves using the dynamic stress layout from {graphlayouts} (layout_as_dynamic()), with a new alpha argument controlling layout stability; other layouts are computed once on the aggregate network and held fixed
  • Changing node composition is now handled properly: every node that ever appears gets a stable position and fades in and out in place as it enters and exits the network
  • New isolates argument ("keep" or "fade") controls whether temporarily isolated nodes stay visible or fade out; keep_isolates is deprecated
  • Dynamic (time-stamped, event-based) networks such as irps_nuclear are now split automatically into cumulative time slices via manynet::to_slices(), so a single dynamic network object passed to grapht() works without manual conversion
  • Interval (spell) networks that record tie begin/end lifespans, such as irps_wwi, are now split automatically into one snapshot per change point showing the ties active in that spell, so grapht(irps_wwi) works directly (previously it errored because such networks are dynamic but carry no time attribute for to_slices()); irps_wwi is now a runnable example in the documentation
  • grapht() now uses the dynamic stress layout by default even for two-mode networks (rather than a hierarchy layout, which collapsed many nodes onto a line), suppresses node labels by default for networks with more than 30 nodes to keep frames legible, and fades densely overlapping ties so they read as a density gradient rather than a solid mass
  • Fixed an error when animating networks whose node names contain non-ASCII characters
  • Waves without any ties are no longer silently dropped
  • Closer visual parity with graphr(): directed networks get arrowheads on segments trimmed at the target node, signed networks distinguish positive/negative ties by linetype and colour, mapped aesthetics use the same palettes with factor levels consistent across frames, and legends transition along with the animation
  • Aesthetic-resolution helpers are now shared between graphr() and grapht() (new R/graph_aes.R), so styling cannot drift between static and animated plots
  • Added a test suite for grapht() (no gif rendering required)
  • Now aborts with a clear message when its input cannot be split into waves or slices, instead of failing much later with a cryptic igraph error (closes #40); the underlying cause — to_waves() silently ignoring a time attribute not named “wave” — will be fixed in {manynet} 2.2.2, and the tutorial example now uses a wave attribute, which splits correctly with {manynet} 2.2.1
• Added an edge_bundle argument to graphr() for bundling edges in dense networks (closes #19):
  • TRUE/"force" uses force-directed bundling, with "path" and "minimal" selecting the other non-hierarchical algorithms
  • colour/width/linetype mappings are preserved and directed networks keep their arrowheads.
  • This wires up ggraph’s non-hierarchical bundling geoms (added in ggraph 2.2.0), which were previously imported but never called, so the ggraph dependency is now (>= 2.2.0)
• Fixed edge_size = 0 not fully suppressing edges on directed networks (closes #50): arrowhead length was hard-coded regardless of edge_size, leaving a visible arrowhead when the line was hidden. Arrow length now scales with the resolved edge width (capped so heavily-weighted edges don’t get oversized heads) and is omitted entirely when the width is 0
• Fixed two-mode auto-shapes assigning circles to the second mode: the first mode now takes circles and the second squares, as intended
• Fixed graphr() returning an empty plot for networks consisting only of isolates (e.g. the empty dyad/triad motifs): isolates are now kept whenever removing them would empty the graph
• Fixed graphs() erroring on lists containing tie-less networks (e.g. plot() on motif censuses): panels sharing a layout now keep isolates so every node has a coordinate in every wave
• Fixed graphr() erroring on weight or size attributes carrying measure classes (e.g. tie_measure results from {netrics} stored as attributes)
• Fixed a vector-recycling warning in graphs()’ ego-network detection

Tutorials

• Fixed the “Tying up loose ends” exercise in the visualisation tutorial erroring on tie_closeness() (closes #39): the tutorial now loads {netrics} and uses its measure functions (tie_by_closeness(), tie_is_triangular()), and every tutorial code chunk is now exercised by the functional tests below
• Reworked the “Visualising Networks” tutorial to match the structure and features of the {manynet} v2.2 tutorials
  • Rebranded the tutorial in autograph red, with larger, more readable text and matching ‘Run code’ buttons
  • Added a checkbox Aims section, “Catching up”, “Going further”, “Beginner note”, and “In brief” callout boxes, per-page mini-tables of contents, and free play sections with a choose-your-own-data difficulty ladder
  • Added hover-over glossary terms throughout and a closing Summary section with a function overview table and glossary
  • Added quiz questions with feedback, and hints for the coding exercises
  • New coverage of edge_bundle, label_repel/label_dist, the isolates argument, snap grid-snapping, autograph’s own special-purpose layouts, and programmatic export with ggsave()
  • New sections on directed networks (automatic, width-scaled arrowheads and manual control via edge_size), automatic mode shapes in two-mode networks, and manually adjusting a layout’s coordinate table before passing it back via x/y
  • Added artist-themed gifs throughout, including as quiz-answer feedback
• Added a static, read-only version of the tutorial as a pkgdown article (“Tutorials” menu on the website), as in {manynet}
• Added functional testing of all tutorial code chunks (tests/testthat/test-tutorials_autograph.R), mirroring {manynet}’s tutorial testing infrastructure

Layouts

• Fixed layout_tbl_graph_layered() ordering nodes by the names rather than the positions of their neighbours in adjacent layers, which degraded every barycenter sweep to NA and raised warnings
• Replaced deprecated dplyr::case_match() with dplyr::recode_values()

Plotting

• Fixed plot.matrix() erroring when no membership argument was supplied, for both one-mode and two-mode matrices

autograph 1.0.3

Plotting

• Fixed the error produced by a namespace reference in a call in ergm_res by serializing it, moving to extdata, and loading it via load_ergm_res()

autograph 1.0.2

Plotting

• Fixed the error produced by a namespace reference in a call in ergm_res

autograph 1.0.1

Package

• Updated the logo

Plotting

• Fixed the error in some flavours by removing environment references in included objects
• Closed #44 by adding example that uses ggplot2::scale_colour_discrete() to tweak colour output

Tutorials

• Fixed the tutorial to use netrics functions

autograph 1.0.0

Package

• Updated startup message to declare the set theme

Graphing

• Improved node_shape to accept more categories
• Moved node_is_isolate and node_adoption_time to internal helpers to reduce dependencies
• Fixed #47 by overriding shape to fillable (21)
• Fixed #10 and #52 by adding label distance parameter
• Fixed #17 and #40 by improving grapht()

Plotting

• Closed #37 by adding EgoAlter sienaGOF plot
• Fixed #36 by using .to_factor() in plot.ag_gof() to correct numeric ordering of statistics, and dropped cumulative correction in plot.sienaGOF()
• Fixed #38 by dropping linetype in favour of colours even for bw theme in plot.influenceTable()
• Fixed option reference from snet_theme to stocnet_theme in plot.selectionTable() and plot.influenceTable()
• Applied ag_font() to migraph model plots for consistent typography
• Reorganised plot scripts by purpose: summaries, tests, and analysis
• Fixed #46 by not appending “X” to the names when creating the data frame and moving factor coercion later in the process

Tutorial

• Fixed #41 by updating tutorials to use fill aesthetics (scale_fill_*()) instead of colour aesthetics (scale_colour_*())

autograph 0.6.0

Package

• Updated logo

Graphing

• graphr() now auto-dispatches to graphs() when passed a list of graphs
• graphs() no longer requires {patchwork} to be loaded separately
• Closed #12 by changing node aesthetics from color to fill using fillable shape codes (21–25) for nodes to support fill-based colour scales
• Consolidated legend modifications into internal graph_legends() helper
• Improved legend labelling:
  • edge sign legend now labelled “Sign”
  • edge weight/width now labelled “Weight”/“Width”
  • node mode/shape legend now labelled “Mode”/“Shape”
• Closed #8 by adding “isolates” argument to graphr():
  • "legend" (default) removes isolates from the graph but notes them in the legend
  • "caption" removes isolates from the graph but notes them in the caption
  • "keep" retains isolates in the graph as-is (closes #12)

Theming

• Removed scale_*() functions as redundant with better theme support and match_color()

Layouts

• Replaced {Rgraphviz} (Bioconductor) with igraph::layout_with_sugiyama for Sugiyama/hierarchy layouts, removing the Bioconductor dependency
• Improved Sugiyama layout with dummy node insertion and barycenter crossing minimisation for better edge routing
• Fixed #18 for lattice layout snapping by rotating the layout to optimise edge verticality and horizontality

autograph 0.5.1

Plotting

• Improved plot.gof.ergm() (closes #31)
  • Now works on directed and two-mode networks and dyadwise shared partners
  • Now has more informative error message if statistic not available
  • Now accepts more descriptive and gof-formula consistent statistic names

autograph 0.5.0

Package

• Shortened startup messages

Plotting

• Added plot.goldfish.changepoints()
• Added plot.goldfish.outliers()
• Added plot.mnet() to avoid igraph::plot.igraph() dispatching

Graphing

• Restructured scripts for improved maintenance and development in the future
• Fixed ggplot2::geom_violin() call in graphr() to avoid warnings with ggplot2 v4.0.0
• Improved graphr() internals to rely on a NULL “layout” parameter and .infer_layout()
• Improved graphr() to use match_color() for diffusion palettes
• Fixed graphs() handling of changing networks

autograph 0.4.2

Package

• Added ggpizzas to README

Plotting

• Fixed node overflow issue and restored marginal density plot in plot.ag_conv() by dropping +.ggplot()
• Added automatic legend labelling where node_size or node_color or edge_color is given

Theming

• Added “hwu” theme for Heriot-Watt University
• Improved highlight and divergent theme setting to use switch
• Added some discussion about colour-blindedness to palettes documentation and viz tute
• Added some instruction on how to customise themes more specifically

autograph 0.4.1

Package

• Improved startup message to ignore class

Theming

• Added “iast” theme for the Institute of Advanced Studies, Toulouse

Plotting

• Improved ergm convergence diagnostic plotting by working on the results object, mostly avoiding startup conflict warning
• Dropped marginal density plot in plot.ag_conv() to fix {ggplot2} v4.0.0-related node overflow issue

autograph 0.4.0

Package

• Fixed DOI in CITATION
• Improved README introduction
• Improved README graphing illustration, including igraph comparison figure
• Improved README plotting illustration, added SAOM/ERGM GOF comparison figure

Theming

• Improved stocnet_theme() documentation
• Improved stocnet_theme() to register a font family for plots
  • A vector of potential fonts is included for some themes
  • The first font found on the system will be used, and user notified
  • If no fonts are found, the default R font (“sans”) will be used
  • A message is printed to inform the user if the default is used, and how to install missing fonts via {extrafont}
• Added font options for “iheid”, “oxf”, “ethz”, “uzh”, and “rug” themes
• Added ag_font() for retrieving the registered font family
• Improved match_colors() documentation
• Exported is_dark() and made it vectorised
• Added match_colors() and is_dark() tests
• Dropped theme_*() functions in favour of stocnet_theme()
• Dropped theme_*() tests
• Added stocnet_theme() tests
• Added “cmu” theme for Carnegie Mellon University

Graphing

• Improved graphr() by using registered fonts where available
• Improved graphr() by using ag_qualitative() for discrete colour scales

Plotting

• Improved plot.selectionTable() and plot.influenceTable() documentation by consolidating them together into one help file
• Improved plot.ag_conv(), plot.ag_gof(), and plot_interp by using registered fonts where available
• Improved plot.sienaGOF() to use lower case auxiliary statistic description

Data

• Renamed res_monan_traces to monan_conv
• Renamed res_monan_gof to monan_gof
• Renamed res_ergm_gof to ergm_gof
• Renamed res_siena_gof to siena_gof
• Renamed res_siena_influence to siena_influence
• Renamed res_siena_selection to siena_selection

autograph 0.3.1

Package

• Fixed old citation style issue for CRAN

Plotting

• Added plot.ag_conv() as a new plotting method for convergence diagnostics
  • Plots MCMC traces as a line plot with loess smoothing highlighting the trend
  • Plots overall density plot of the samples on the right margin
• Improved plotting of {MoNAn} trace objects by using plot.ag_conv()
• Added plot.mcmc.list() for plotting MCMC samples from ergm::ergm results objects, using plot.ag_conv()

Data

• Added ergm_res for testing and illustration of plot.mcmc.list(), use ergm_res$sample to access the MCMC sample

autograph 0.3.0

Package

• Added package documentation
• Added citation
• Dropped dependencies {tidyr}, {cli}, and {concaveman}
• Added more description to the function overview sections on the website
• Added CODECOV_TOKEN to Github secrets for test coverage reporting

Graphing

• Fixed graphr() not using theme colours for node and edge aesthetics

Plotting

• Added new plot class and method for centralising GOF plotting
  • Improved plot.sienaGOF() and plot.gof.stats.monan() to use new plotting method
  • Added plot.gof.ergm() for plotting ERGM GOF objects
  • Improved GOF plotting by adding boxplot within the violins
  • Improved GOF plotting by adding crosses for outliers
  • Improved GOF plotting by adding dashed line for 0.05 and 0.95 quantile bounds
  • Improved GOF plotting by dropping statistics without variance
  • Improved GOF plotting by using cumulative = FALSE by default
• Fixed issue with pre-v1.3.20 RSiena::gof() objects, thanks @TomSnijders
• Added testing of GOF plotting
• Added testing of measures plotting

Theming

• Added set_stocnet_theme() alias for stocnet_theme()
• Fixed issue with ‘oxf’ and ‘unige’ themes not being recognised

Data

• Added res_ergm_gof for testing and illustration of plot.gof.ergm()

Tutorial

• Added visualisation tutorial from manynet
  • Improved introduction
  • Improved section on titles, labels, and legends
  • Improved section explaining base and grid graphics
  • Added section demonstrating difference between igraph::plot(), ggraph::ggraph(), and graphr()
  • Added table describing the main arguments of graphr() and the visualisation dimensions to which they relate
  • Added section showing how to use “node_shape” (poorly)
  • Improved section showing how to use “node_colour” and “node_group”
  • Added section showing how to use “node_size”
  • Added section showing how to set a theme
  • Added section showing how to use “edge_colour” and “edge_size”
  • Improved section introducing {patchwork}, graphs(), and grapht()
  • Added plotting section to viz tutorial

autograph 0.2.0

Package

• Added (currently) necessary dependencies
• Removed unnecessary manynet dependencies

Plotting

• Added graphr(), graphs(), and grapht() from manynet for quick plotting of one or more graphs
• Improved +.ggplot() to check whether second object inherits ggplot class (thanks @teunbrand for fixing #110)
• Fixed issue with edge_linetype in signed, directed networks with weights (closed #14)
• Updated README with examples of graphr() and others

Themes

• Added themes for Oxford and UNIGE (closed #1)
• Improved stocnet_theme() to add option to “stocnet_theme” (previously “snet_theme”)
• Added is_dark() to check whether a theme is dark or light
• Added match_color() to return closest matching colors from a palette

Layouts

• Added layout_valence() for signed graphs (closed #6)
• Added configurational layouts from manynet
• Added aliases for various layout_tbl_graph_*() functions

autograph 0.1.2

Package

• Fixed line break issues in DESCRIPTION

Themes

• Fixed default for ag_sequential()

Layouts

• Fixed “layout_layered” to accept typical ggraph parameters

manynet

• Added return value statements

migraph

• Added return value statements

RSiena

• Added return value statements

MoNAn

• Added plot.traces.monan()
• Added plot.gof.stats.monan()

autograph 0.1.1

Package

• Fixed DESCRIPTION issues

autograph 0.1.0

Package

• Initial setup, with all the goodies

Theming

• Added stocnet_theme() for setting a theme that can then be reused across successive plots (closes #3)
  • For example, stocnet_theme("iheid") for IHEID colour theme
• Added ag_*() palettes, for example:
  • ag_highlight() to select the highlight colours of a particular palette
• Added match_color() for matching one or more hexcodes to a palette’s offerings

Plotting

• Added manynet plot methods
  • Added plot.diff_model()
  • Added plot.matrix()
  • Added plot.learn_model()
  • Added plot.network_measures()
  • Added plot.network_motif()
  • Added plot.tie_measure()
  • Added plot.node_measure()
  • Added plot.node_member()
  • Added plot.node_members()
  • Added plot.node_motif()
• Added migraph plot methods
  • Added plot.netlm()
  • Added plot.netlogit()
  • Added plot.network_test()
  • Added plot.diffs_model()
• Added RSiena plot methods
  • Added plot.sienaGOF()
  • Added plot.influenceTable()
  • Added plot.selectionTable()

Layouts

• Added layout_tbl_graph_matching() for positioning nodes according to their manynet::to_matching() partners
• Added first version of layout_tbl_graph_layered() for layering nodes according to a Sugiyama-type layout

Data

• Added some precooked results for testing and illustration