# autograph 1.2.2

## 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

# 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` <character> and `..2` <logical>") 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
