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