Check compatibility with development glmmTMB and brms

.github/scripts/check-development-backend.R

@@ -0,0 +1,76 @@
+# A compatibility smoke test, not a check of parameter recovery or MCMC accuracy.
+backend <- commandArgs(trailingOnly = TRUE)
+stopifnot(length(backend) == 1L, backend %in% c("glmmTMB", "brms"))
+description <- utils::packageDescription(backend)
+message(backend, " ", description$Version)
+if (!is.null(description$RemoteSha)) message("Upstream commit: ", description$RemoteSha)
+
+set.seed(91)
+data <- expand.grid(member = c(-1, 1), occasion = 1:3, coupleID = 1:20)
+data$coupleID <- factor(data$coupleID)
+shared <- stats::rnorm(20, sd = 0.8)
+difference <- stats::rnorm(20, sd = 0.5)
+data$outcome <- shared[data$coupleID] + data$member * difference[data$coupleID] +
+  stats::rnorm(nrow(data), sd = 0.4)
+data <- dyadMLM::prepare_dyad_data(
+  data, dyad = coupleID, member = member, time = occasion,
+  model_types = "none", seed = 91
+)
+
+# Repeated observations identify stable dyad effects separately from residual sigma.
+formula <- outcome ~ 1 + (1 | coupleID) +
+  (0 + .member_contrast_arbitrary | coupleID)
+if (backend == "glmmTMB") {
+  model <- glmmTMB::glmmTMB(formula, data = data)
+  stopifnot(model$fit$convergence == 0L, isTRUE(model$sdr$pdHess))
+  covariance <- glmmTMB::VarCorr(model)$cond
+  shared_variance <- covariance[[1L]][1L, 1L]
+  difference_variance <- covariance[[2L]][1L, 1L]
+} else {
+  # Twenty retained draws exercise real extraction; they are not for inference.
+  # Keep warnings visible. Compilation can take longer than this short sampling run.
+  model <- brms::brm(
+    formula, data = data, backend = "rstan",
+    prior = c(
+      brms::set_prior("normal(0, 2)", class = "Intercept"),
+      brms::set_prior("exponential(1)", class = "sd"),
+      brms::set_prior("exponential(1)", class = "sigma")
+    ),
+    chains = 1, cores = 1, iter = 120, warmup = 100,
+    init = 0, seed = 91, refresh = 0
+  )
+  standard_deviations <- brms::VarCorr(model, summary = FALSE)$coupleID$sd
+  stopifnot(nrow(standard_deviations) == 20L)
+  shared_variance <- standard_deviations[, "Intercept"]^2
+  difference_variance <- standard_deviations[, ".member_contrast_arbitrary"]^2
+}
+
+# Independent reference calculation from public backend output, draw by draw.
+member_variance <- shared_variance + difference_variance
+member_covariance <- shared_variance - difference_variance
+expected_varcov <- expected_sdcor <- array(NA_real_, c(length(member_variance), 2, 2))
+expected_varcov[, 1, 1] <- expected_varcov[, 2, 2] <- member_variance
+expected_varcov[, 1, 2] <- expected_varcov[, 2, 1] <- member_covariance
+expected_sdcor[, 1, 1] <- expected_sdcor[, 2, 2] <- sqrt(member_variance)
+expected_sdcor[, 1, 2] <- expected_sdcor[, 2, 1] <- member_covariance / member_variance
+if (backend == "glmmTMB") {
+  expected_varcov <- expected_varcov[1, , ]
+  expected_sdcor <- expected_sdcor[1, , ]
+}
+
+recovered <- dyadMLM::recover_exchangeable_covariance(model, posterior = "draws")
+stopifnot(inherits(recovered, "exchangeable_covariance"), length(recovered) == 1L)
+assert_equal <- function(actual, expected) {
+  stopifnot(all(is.finite(actual)))
+  stopifnot(isTRUE(all.equal(unname(actual), unname(expected), tolerance = 1e-10)))
+}
+assert_equal(recovered[[1L]]$varcov, expected_varcov)
+assert_equal(recovered[[1L]]$sdcor, expected_sdcor)
+
+if (backend == "brms") {
+  # In particular, average each draw's correlation, not the averaged variances.
+  posterior_mean <- dyadMLM::recover_exchangeable_covariance(model)
+  assert_equal(posterior_mean[[1L]]$varcov, apply(expected_varcov, c(2, 3), mean))
+  assert_equal(posterior_mean[[1L]]$sdcor, apply(expected_sdcor, c(2, 3), mean))
+}
+message(backend, " covariance extraction and recovery passed.")

.github/workflows/dependency-canary.yaml

@@ -0,0 +1,68 @@
+name: Development dependencies
+
+on:
+  schedule:
+    - cron: "23 7 * * 1"
+  workflow_dispatch:
+  pull_request:
+    paths:
+      - .github/workflows/dependency-canary.yaml
+      - .github/scripts/check-development-backend.R
+
+permissions:
+  contents: read
+
+jobs:
+  dependency-canary:
+    name: Development ${{ matrix.backend }}
+    runs-on: ubuntu-latest
+    timeout-minutes: 40
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - backend: glmmTMB
+            package: glmmTMB/glmmTMB/glmmTMB
+          - backend: brms
+            package: paul-buerkner/brms
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v7
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: release
+
+      # Override the backend without installing all of its optional dependencies.
+      - name: Select development backend
+        shell: Rscript {0}
+        run: |
+          cat("Remotes: ${{ matrix.package }}\n", file = "DESCRIPTION", append = TRUE)
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::BH
+            any::RcppEigen
+            any::rcmdcheck
+            local::.
+          needs: check
+
+      - name: Restore package metadata
+        run: git restore DESCRIPTION
+
+      # RStan needs BH and RcppEigen headers even when installed as a binary.
+      - name: Fit model and verify covariance recovery
+        run: Rscript .github/scripts/check-development-backend.R ${{ matrix.backend }}
+
+      # These runs report upstream breakage but are not required merge checks.
+      - name: Check package with development dependency
+        uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -43,6 +43,7 @@ jobs:
             any::report
             any::RSA
             any::see
+            any::svglite
             any::tidyr
             any::wbCorr
             local::.