Post-CRAN development and 2026 workshop materials

.Rbuildignore

@@ -17,3 +17,6 @@
 ^codecov\.yml$
 ^cran-comments\.md$
 ^CRAN-SUBMISSION$
+^tmp$
+^Rplots\.pdf$
+^dyadMLM_.*\.tar\.gz$

.github/scripts/export-workshop-slides.sh

@@ -0,0 +1,59 @@
+#!/usr/bin/env bash
+
+set -euo pipefail
+
+repository_root="$(cd "${1:-.}" && pwd)"
+workshop_output="${repository_root}/docs/workshop"
+decktape_image="ghcr.io/astefanutti/decktape:3.16.1@sha256:66f5eff34a444628f5ab524da5390a454412fa879f3d15df96daf4c5c8da6b33"
+temporary_root="$(mktemp -d /tmp/dyadmlm-decktape.XXXXXX)"
+temporary_input="${temporary_root}/input"
+temporary_output="${temporary_root}/output"
+
+cleanup() {
+  rm -rf -- "${temporary_root}"
+}
+trap cleanup EXIT
+
+mkdir -p "${temporary_input}" "${temporary_output}" "${workshop_output}"
+
+# DeckTape runs as a non-root user whose UID may differ from the host runner.
+# This directory is temporary and contains only the generated PDFs.
+chmod 0777 "${temporary_output}"
+
+# Give the container only the publication-bound slide files.
+cp "${repository_root}/dev/workshop/dyad-day.html" \
+  "${temporary_input}/dyad-day.html"
+cp "${repository_root}/dev/workshop/applied-tutorial.html" \
+  "${temporary_input}/applied-tutorial.html"
+
+# Fragments are intentionally disabled (DeckTape's default), yielding one PDF
+# page per Reveal slide with ordinary fragments fully revealed.
+docker run --rm \
+  --volume "${temporary_input}:/slides:ro,Z" \
+  --volume "${temporary_output}:/output:Z" \
+  "${decktape_image}" reveal \
+  --size 1050x700 \
+  --pause 1500 \
+  --load-pause 2000 \
+  --chrome-arg=--allow-file-access-from-files \
+  "file:///slides/dyad-day.html" \
+  "/output/01_conceptual_foundations.pdf"
+
+docker run --rm \
+  --volume "${temporary_input}:/slides:ro,Z" \
+  --volume "${temporary_output}:/output:Z" \
+  "${decktape_image}" reveal \
+  --size 1050x700 \
+  --pause 1500 \
+  --load-pause 2000 \
+  --chrome-arg=--allow-file-access-from-files \
+  "file:///slides/applied-tutorial.html" \
+  "/output/02_applied_tutorial.pdf"
+
+test -s "${temporary_output}/01_conceptual_foundations.pdf"
+test -s "${temporary_output}/02_applied_tutorial.pdf"
+
+install -m 0644 "${temporary_output}/01_conceptual_foundations.pdf" \
+  "${workshop_output}/01_conceptual_foundations.pdf"
+install -m 0644 "${temporary_output}/02_applied_tutorial.pdf" \
+  "${workshop_output}/02_applied_tutorial.pdf"

.github/workflows/pkgdown.yaml

@@ -4,8 +4,6 @@ on:
   push:
     branches: [main, master]
   pull_request:
-  release:
-    types: [published]
   workflow_dispatch:
 
 name: pkgdown
@@ -24,26 +22,137 @@ jobs:
       contents: write
     steps:
       - uses: actions/checkout@v7
+        with:
+          fetch-depth: 0
+
+      - name: Determine whether workshop materials changed
+        id: workshop-changes
+        shell: bash
+        env:
+          EVENT_NAME: ${{ github.event_name }}
+          BEFORE_SHA: ${{ github.event.before }}
+          BASE_SHA: ${{ github.event.pull_request.base.sha }}
+          PR_HEAD_SHA: ${{ github.event.pull_request.head.sha }}
+          HEAD_SHA: ${{ github.sha }}
+        run: |
+          rebuild=true
+          # Paths that directly define the published workshop outputs.
+          workshop_paths=(
+            dev/workshop
+            vignettes/diagram-helpers.Rinc
+            vignettes/dim-grid.Rinc
+            vignettes/references.bib
+            pkgdown/templates/content-workshop.html
+            _pkgdown.yml
+            .github/scripts/export-workshop-slides.sh
+            .github/workflows/pkgdown.yaml
+          )
+
+          if [[ "$EVENT_NAME" == "push" && ! "$BEFORE_SHA" =~ ^0+$ ]]; then
+            if git diff --quiet "$BEFORE_SHA" "$HEAD_SHA" -- \
+              "${workshop_paths[@]}"; then
+              rebuild=false
+            fi
+          elif [[ "$EVENT_NAME" == "pull_request" ]]; then
+            if git diff --quiet "$BASE_SHA...$PR_HEAD_SHA" -- \
+              "${workshop_paths[@]}"; then
+              rebuild=false
+            fi
+          fi
+
+          echo "rebuild=$rebuild" >> "$GITHUB_OUTPUT"
 
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, local::.
+          extra-packages: |
+            any::DHARMa
+            any::digest
+            any::ggplot2
+            any::gridExtra
+            any::modelbased
+            any::parameters
+            any::patchwork
+            any::pkgdown
+            any::report
+            any::RSA
+            any::see
+            any::tidyr
+            any::wbCorr
+            local::.
           needs: website
 
+      - uses: quarto-dev/quarto-actions/setup@v2
+
+      - name: Render all workshop materials
+        if: steps.workshop-changes.outputs.rebuild == 'true'
+        run: |
+          quarto render dev/workshop/dyad-day.qmd
+          quarto render dev/workshop/applied-tutorial.qmd
+
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
+      - name: Export workshop slides to PDF
+        if: steps.workshop-changes.outputs.rebuild == 'true'
+        run: bash .github/scripts/export-workshop-slides.sh
+
       - name: Add workshop materials
+        if: steps.workshop-changes.outputs.rebuild == 'true'
         run: |
           mkdir -p docs/workshop/conceptual docs/workshop/applied
           Rscript -e 'pkgdown::render_page(".", "workshop", data = list(pagetitle = "Workshop", description = "Dyadic Data Analysis workshop materials."), path = "workshop/index.html", depth = 1)'
           cp dev/workshop/dyad-day.html docs/workshop/conceptual/index.html
           cp dev/workshop/applied-tutorial.html docs/workshop/applied/index.html
+          cp dev/workshop/03_exercises_cross_sectional.Rmd docs/workshop/03_exercises_cross_sectional.Rmd
+          cp dev/workshop/04_exercises_ild.Rmd docs/workshop/04_exercises_ild.Rmd
+          zip -jq docs/workshop/dyadic-data-analysis-workshop.zip \
+            dev/workshop/00_setup.R \
+            docs/workshop/01_conceptual_foundations.pdf \
+            docs/workshop/02_applied_tutorial.pdf \
+            dev/workshop/03_exercises_cross_sectional.Rmd \
+            dev/workshop/04_exercises_ild.Rmd \
+            dev/workshop/dyadic-data.rds \
+            dev/workshop/dyadic-ild-exercise.rds \
+            dev/workshop/dyadic-person-means.rds \
+            dev/workshop/helpers.R \
+            dev/workshop/hints.R
+
+      - name: Preserve previously published workshop materials
+        if: >-
+          steps.workshop-changes.outputs.rebuild != 'true' &&
+          github.event_name != 'pull_request'
+        run: |
+          git fetch --no-tags --depth=1 origin gh-pages
+          git archive --format=tar \
+            --output=/tmp/dyadmlm-published-workshop.tar \
+            FETCH_HEAD workshop
+          tar -xf /tmp/dyadmlm-published-workshop.tar -C docs
+
+      - name: Validate staged workshop materials
+        if: github.event_name != 'pull_request' || steps.workshop-changes.outputs.rebuild == 'true'
+        shell: bash
+        run: |
+          workshop_files=(
+            docs/workshop/index.html
+            docs/workshop/conceptual/index.html
+            docs/workshop/applied/index.html
+            docs/workshop/01_conceptual_foundations.pdf
+            docs/workshop/02_applied_tutorial.pdf
+            docs/workshop/03_exercises_cross_sectional.Rmd
+            docs/workshop/04_exercises_ild.Rmd
+            docs/workshop/dyadic-data-analysis-workshop.zip
+          )
+
+          for workshop_file in "${workshop_files[@]}"; do
+            test -s "$workshop_file"
+          done
+
+          unzip -tq docs/workshop/dyadic-data-analysis-workshop.zip
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'

.gitignore

@@ -9,3 +9,6 @@ HANDOFF.md
 docs
 /dyadMLM_*.tar.gz
 /*.Rcheck/
+/Rplots.pdf
+/dev/workshop/temp_audit/
+/dev/workshop/applied-tutorial_cache/

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dyadMLM
 Title: Tools for Dyadic Multilevel Models
-Version: 0.1.0
+Version: 0.1.0.9000
 Authors@R: 
     person("Pascal", "Küng", , "kueng.pascal@gmail.com",
            role = c("aut", "cre", "cph"),

NAMESPACE

@@ -3,7 +3,8 @@
 S3method(print,dyadMLM_data)
 S3method(print,dyadMLM_model_comparison)
 S3method(print,exchangeable_rescov)
-export(compare_nested_glmmTMB_models)
+S3method(summary,dyadMLM_data)
+export(compare_nested_models)
 export(prepare_dyad_data)
 export(recover_exchangeable_covariance)
 importFrom(rlang,":=")

NEWS.md

@@ -1,3 +1,35 @@
+# dyadMLM (development version)
+
+* Retained generated columns now use a single leading dot instead of `.dy_`
+  for more readable model formulas; for example, `.dy_x_actor` becomes
+  `.x_actor`. The `.dy_` prefix is reserved for temporary implementation
+  columns.
+* `prepare_dyad_data()` now uses compact composition-column names when the
+  final data contain one composition, such as `.is_female` and
+  `.member_contrast_arbitrary`. Set `short_colnames = FALSE` to retain
+  composition-qualified names. `recover_exchangeable_covariance()` recognizes
+  both forms.
+* `prepare_dyad_data(include_arbitrary_member_contrast = TRUE)` can now add arbitrary
+  member contrasts for distinguishable compositions without changing their
+  metadata or role indicators. This supports full and
+  exchangeability-constrained APIMs from the same prepared data.
+  `set_exchangeable_compositions` still performs reclassification for pooling
+  and DIM preparation.
+* Added a `summary()` method for prepared data that prints the dyadic structure
+  followed by standard summaries of all columns.
+* Generated-column tracking now records all retained composition and modeling
+  columns. Printing and model comparison use these records rather than
+  inferring column ownership from a prefix, and generated names are checked for
+  collisions and valid R syntax before they are written.
+* `prepare_dyad_data(add_apim_gmc_predictors = TRUE)` now adds GMC source,
+  actor, and partner columns alongside raw APIM columns, plus lagged variants
+  when requested. It uses one mean over retained non-missing values, warns
+  about skipped non-numeric predictors in mixed selections, and leaves DIM/DSM
+  centering unchanged.
+* Renamed `compare_nested_glmmTMB_models()` to `compare_nested_models()`.
+* Added package-level help at `?dyadMLM`, with links to the main functions,
+  example datasets, and getting-started documentation.
+
 # dyadMLM 0.1.0
 
 * Initial release.

R/add_actor_partner_columns.R

@@ -6,8 +6,8 @@
 #' predictors, this will create actor and partner versions of the raw predictor
 #' and each recorded predictor component, such as the within-person and
 #' between-person components created by [center_predictors()].
-#' Selected lag predictors additionally create lag-1 raw and within-person
-#' actor and partner columns.
+#' Selected lag predictors also create actor and partner columns for eligible
+#' lagged components.
 #'
 #' The function will use the predictor decomposition metadata stored in
 #' `attr(data, "dyadMLM")$temporal_decompositions`, so downstream code does
@@ -69,7 +69,7 @@ add_actor_partner_columns <- function(data) {
     }
     if (component == "raw") {
       predictor_suffix <- make_dyad_suffixes(predictor)[[predictor]]
-      column_stem <- paste0(dyad_reserved_prefix, predictor_suffix)
+      column_stem <- paste0(dyad_retained_prefix, predictor_suffix)
     }
 
     lag_suffix <- make_predictor_lag_suffix(lag)
@@ -94,15 +94,19 @@ add_actor_partner_columns <- function(data) {
       temporal_component = apim_predictors$component,
       lag = apim_predictors$lag,
       model_family = "apim",
-      column_role = "actor"
+      column_role = "actor",
+      variable_role = "predictor",
+      source_column = apim_predictors$source_column
     ),
     tibble::tibble(
       target = apim_predictors$partner_column,
       predictor = apim_predictors$predictor,
       temporal_component = apim_predictors$component,
       lag = apim_predictors$lag,
       model_family = "apim",
-      column_role = "partner"
+      column_role = "partner",
+      variable_role = "predictor",
+      source_column = apim_predictors$source_column
     )
   )
   validate_generated_column_plan(out, apim_plan)
@@ -172,6 +176,7 @@ add_actor_partner_columns <- function(data) {
   }
 
   attr(out, "dyadMLM")$apim_predictors <- apim_predictors
+  out <- record_generated_columns(out, apim_plan)
 
   return(out)
 }