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