Release v1.3.1: modern theme refresh + network type

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,54 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Runs R CMD check --as-cran across the standard CRAN platform matrix on every
+# push and PR targeting main/master only. Dev-side checks are run manually
+# by the maintainer; CI gates only the final mile into master.
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+          args: 'c("--no-manual", "--as-cran")'

DESCRIPTION

@@ -1,22 +1,22 @@
 Package: panelView
 Type: Package
 Title: Visualizing Panel Data
-Version: 1.2.1
-Date: 2026-03-20
+Version: 1.3.1
+Date: 2026-05-13
 Authors@R: 
   c(person("Yiqing", "Xu", ,"yiqingxu@stanford.edu", role = c("aut", "cre"), 
   comment = c(ORCID = "0000-0003-2041-6671")),
   person("Hongyu", "Mou", , "hongyumou@g.ucla.edu", role = c("aut")), 
   person("Licheng", "Liu", ,"liulch@mit.edu", role = c("aut")))
 Maintainer: Yiqing Xu <yiqingxu@stanford.edu>
-Description: Visualizes panel data. It has three main functionalities: (1) it plots the treatment status and missing values in a panel dataset; (2) it visualizes the temporal dynamics of a main variable of interest; (3) it depicts the bivariate relationships between a treatment variable and an outcome variable either by unit or in aggregate. For details, see <doi:10.18637/jss.v107.i07>.
+Description: Visualizes panel data. It has four main functionalities: (1) it plots the treatment status and missing values in a panel dataset; (2) it visualizes the temporal dynamics of a main variable of interest; (3) it depicts the bivariate relationships between a treatment variable and an outcome variable either by unit or in aggregate; (4) it displays the network structure of multi-way fixed effects as a k-partite graph, identifying connected components, singletons, and duplicate observations. For details, see <doi:10.18637/jss.v107.i07>.
 URL: https://yiqingxu.org/packages/panelview/, https://github.com/xuyiqing/panelView
 BugReports: https://github.com/xuyiqing/panelView/issues
 License: MIT + file LICENSE
 Imports: ggplot2 (>= 3.4.0), gridExtra, grid, dplyr (>= 1.0.0)
 Depends: R (>= 2.10)
 Encoding: UTF-8
-Suggests: testthat (>= 3.0.0)
+Suggests: testthat (>= 3.0.0), igraph
 RoxygenNote: 7.3.2
 LazyData: true
 Config/testthat/edition: 3

NAMESPACE

@@ -1,6 +1,7 @@
 ##useDynLib(panelView)
 ##exportPattern("^[[:alpha:]]+")
-importFrom("stats", "na.omit", "sd", "var", "ave", "aggregate", "approxfun")
+importFrom("stats", "na.omit", "sd", "var", "ave", "aggregate", "approxfun",
+           "setNames")
 importFrom("ggplot2", "geom_boxplot", "geom_density", "geom_tile",
            "geom_point","geom_col", "labs", "theme_bw", "scale_fill_manual",
            "geom_hline", "geom_line", "geom_ribbon", "geom_vline",
@@ -12,6 +13,8 @@ importFrom("ggplot2", "geom_boxplot", "geom_density", "geom_tile",
            "guide_legend", "margin", "guides","xlab","ylab", "unit",
            "element_rect", "geom_jitter", "scale_shape_manual", "geom_bar",
            "scale_fill_gradient", "sec_axis", "facet_wrap")
+importFrom("ggplot2", "geom_segment", "geom_polygon", "geom_text")
+importFrom("grDevices", "chull")
 importFrom("gridExtra", "grid.arrange", "arrangeGrob")
 importFrom("grid", "textGrob", "gpar")
 importFrom("dplyr", "coalesce", "summarise", "group_by_all", "n")

NEWS.md

@@ -0,0 +1,149 @@
+# panelView 1.3.1
+
+## Visual refresh
+
+* Plot defaults updated for a cleaner, publication-ready look across all four
+  plot types: plain left-aligned titles, base font size 11, white background
+  for status heatmaps, subtle major-x gridlines for trajectories, and a thin
+  gray dashed treatment-onset marker (replaces the prior thick white line).
+* Multi-level discrete treatment palette refreshed to a muted, perceptually
+  distinct sequence; binary and continuous palettes unchanged.
+* Control-trajectory gray lightened to `grey75` so dense overlaps no longer
+  darken into a near-black band.
+
+## New arguments
+
+* `theme = c("default", "red")`: optional theme switch. `"red"` activates a
+  high-contrast publication recipe with gray control / brick-red treated-post
+  for status and outcome plots and a solid black dashed treatment-onset line.
+* `group.mean.overlay = FALSE`: opt-in for the outcome plot. Dims per-unit
+  trajectories and overlays a heavy group-mean line plus a 10--90% quantile
+  ribbon per group. Currently scoped to the main DID continuous-outcome path.
+
+## Deprecations
+
+* `theme.bw = FALSE` is soft-deprecated and emits a one-time warning. The
+  legacy gray-panel look is no longer demonstrated in the tutorial and may
+  be removed in a future major release.
+
+# panelView 1.3.0
+
+## New features
+
+* Add `type = "network"` to visualize the connectivity structure of multi-way
+  fixed effects as a k-partite graph (Correia 2016). The new plot identifies
+  singletons, connected components, and non-unique (duplicate) observations via
+  weighted edges, and supports two or more fixed-effect dimensions as well as
+  formula-based missingness.
+* New parameters for the network plot: `show.singletons`,
+  `highlight.components`, `layout`, `node.size`, `show.labels`, `edge.color`,
+  `edge.alpha`, `edge.width`, and `singleton.color`.
+* Add `igraph` to `Suggests` (used only by `type = "network"`).
+* Add a new tutorial chapter (chapter 4) documenting the network
+  visualization, and expand the Quarto tutorial index and references.
+
+## Improvements
+
+* Update tutorial chapter 1 and use consistent `U`-prefix naming for simulated
+  units in chapter 4.
+* Update `DESCRIPTION` to describe the new k-partite graph functionality.
+
+# panelView 1.2.1
+
+## Bug fixes
+
+* Remove spurious runtime warnings: fix deprecated `group_by_all()` by
+  switching to `group_by(across(everything()))`; drop unused
+  `position = "identity"` and `stat = "identity"` in ggplot2 layers.
+* Fix a `margin()` vector-argument warning and a false-positive `by.cohort`
+  warning.
+* Address ggplot2 `size` deprecation and tighten `class()` comparisons.
+* Fix a bivariate plot title bug.
+
+## Internal
+
+* Refactor monolithic `panelView.R` into focused plot files (one file per plot
+  type).
+* Add a testthat suite (36 tests).
+* Replace the legacy vignette with a Quarto-based manual and add a changelog
+  chapter.
+* Add `ARCHITECTURE.md` with Mermaid diagrams documenting the package
+  structure.
+* `R CMD check --as-cran`: 0 errors, 0 warnings, 0 notes.
+
+# panelView 1.1.17
+
+Add links to the [JSS paper](https://doi.org/10.18637/jss.v107.i07).
+
+# panelView 1.1.16
+
+* Add `collapse.history` to allow users to collapse units by treatment history
+  in a `treat` plot.
+* Add `show.missing` to output missing-data summary statistics for the key
+  variables.
+* Add `axis.lab.angle` to allow users to change the angle of the x-axis
+  labels.
+* Allow `pre.post` to be applied to an `outcome` plot.
+* Change the color scheme in the `outcome` plot.
+* Miscellaneous bug fixes.
+
+# panelView 1.1.11
+
+* Add `by.cohort` to plot average outcome trajectories of units sharing the
+  same treatment history (when the number of unique histories is under 20).
+
+# panelView 1.1.10
+
+* Add `by.group.side` to arrange subfigures of `by.group = TRUE` in a row
+  rather than a column.
+* Add `display.all` to show all units when the number of units exceeds 500
+  (otherwise a random sample of 500 units is shown).
+
+# panelView 1.1.8
+
+* Add `leave.gap` to keep gaps in time using white bars when the time variable
+  is unevenly spaced (e.g., due to missing data).
+* Add `type = "missing"` to plot missingness in data.
+
+# panelView 1.1.7
+
+* Rename the main function from `panelView` to `panelview` for consistency
+  with the Stata version.
+* In outcome plots, use a dot to represent the last-period observation of a
+  unit that is treated in the last period.
+
+# panelView 1.1.6
+
+* Plot time series of outcome and treatment in one graph
+  (`type = "bivar"`). By default, plots mean D and Y against time in the same
+  graph; use `by.unit = TRUE` to plot each unit. New `style`, `ylim`, and
+  `lwd` options control line/bar styles, axis limits, and line width.
+
+# panelView 1.1.4
+
+* Add `treat.type` to control whether the treatment variable is treated as
+  continuous (`"continuous"`) or discrete (`"discrete"`).
+
+# panelView 1.1.2
+
+* Rename plot `type`s: `"treat"` (formerly `"missing"`) for treatment status
+  and `"outcome"` (formerly `"raw"`) for raw outcomes.
+* Allow more than two treatment levels.
+* Add `pre.post` to distinguish pre- and post-treatment observations for
+  treated units in a DID setting.
+* Rename `by.treatment` to `by.timing` and `treatment` to `ignore.treat`.
+* Add fontsize options.
+
+# panelView 1.0.5
+
+Fix typos. CRAN release.
+
+# panelView 1.0.4
+
+* Allow plotting treated units on top of control units in the "missing" plot.
+* Streamline the `color` option for both the "missing" and "raw" plots.
+
+# panelView 1.0.3
+
+* Allow changing the color of bricks in the "missing" plot.
+* Allow leaving the treatment blank in both the "missing" and "raw" plots.