Version 1.0.0

.Rbuildignore

@@ -2,7 +2,6 @@
 ^\.Rproj\.user$
 ^README\.Rmd$
 ^cran-comments\.md$
-^NEWS\.md$
 ^\.github$
 ^\.git$
 ^\.gitignore$
@@ -16,5 +15,5 @@
 ^\.pre-commit-config\.yaml$
 ^CRAN-SUBMISSION$
 ^doc$
-^docs$
 ^Meta$
+^\.Rhistory$

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

@@ -1,11 +1,12 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, v1.0.0-dev]
   pull_request:
-    branches: [main, master]
+  workflow_dispatch:
 
-name: R-CMD-check
+name: R-CMD-check.yaml
 
 permissions: read-all
 
@@ -21,37 +22,23 @@ jobs:
         config:
           - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,  r: 'release'}
-          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
-      _R_CHECK_FORCE_SUGGESTS_: false
-      _R_CHECK_CRAN_INCOMING_REMOTE_: false
-      _R_CHECK_CRAN_INCOMING_: false
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - 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
-
-      - name: Install system dependencies (Linux)
-        if: runner.os == 'Linux'
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y libcurl4-openssl-dev libxml2-dev libssl-dev libfontconfig1-dev
-
-      - name: Install system dependencies (macOS)
-        if: runner.os == 'macOS'
-        run: |
-          brew install --cask xquartz
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
@@ -61,7 +48,5 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
-          build_args: 'c("--no-manual", "--compact-vignettes=gs+qpdf")'
-          error-on: '"error"'
-        env:
-          _R_CHECK_FORCE_SUGGESTS_: false
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+          error-on: '"note"'

.github/workflows/pkgdown.yaml

@@ -23,12 +23,9 @@ concurrency:
   cancel-in-progress: false
 
 jobs:
-  pkgdown:
+  # Builds the site for every event; pull requests stop here.
+  build:
     runs-on: ubuntu-latest
-    # Only restrict concurrency for non-PR jobs
-    environment:
-      name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     permissions:
@@ -54,14 +51,28 @@ jobs:
         shell: Rscript {0}
 
       - name: Setup Pages
+        if: github.event_name != 'pull_request'
         uses: actions/configure-pages@v4
 
       - name: Upload artifact
+        if: github.event_name != 'pull_request'
         uses: actions/upload-pages-artifact@v3
         with:
           path: docs
 
+  # The github-pages environment accepts deployments from the default branch
+  # only, so the job that uses it does not run for pull requests.
+  deploy:
+    if: github.event_name != 'pull_request'
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    permissions:
+      pages: write
+      id-token: write
+    steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        if: github.event_name != 'pull_request'
         uses: actions/deploy-pages@v4

.github/workflows/test-coverage.yaml

@@ -2,35 +2,62 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, v1.0.0-dev]
   pull_request:
-    branches: [main, master]
+  workflow_dispatch:
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      # Run the tests skipped on CRAN so that coverage includes them
+      NOT_CRAN: true
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
             install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          print(cov)
+          covr::to_cobertura(cov)
         shell: Rscript {0}
+
+      - uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          files: ./cobertura.xml
+          plugins: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v7
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: BayesianQDM
 Type: Package
-Title: Bayesian Quantitative Decision-Making Framework for Binary and Continuous Endpoints
-Version: 0.1.0
+Title: Bayesian Quantitative Decision-Making Framework for Binary, Continuous and Time-to-Event Endpoints
+Version: 1.0.0
 Authors@R: c(
     person(given  = "Gosuke",
            family = "Homma",
@@ -10,48 +10,44 @@ Authors@R: c(
     person(given  = "Yusuke",
            family = "Yamaguchi",
            role   = c("aut")))
-Description: Provides comprehensive methods to calculate posterior probabilities,
-    posterior predictive probabilities, and Go/NoGo/Gray decision probabilities
-    for quantitative decision-making under a Bayesian paradigm in clinical trials.
-    The package supports both single and two-endpoint analyses for binary and
-    continuous outcomes, with controlled, uncontrolled, and external designs.
-    For single continuous endpoints, three calculation methods are
-    available: numerical integration (NI), Monte Carlo simulation (MC), and
-    Moment-Matching approximation (MM). For two continuous endpoints, a bivariate
-    Normal-Inverse-Wishart conjugate model is implemented with MC and MM methods.
-    For two binary endpoints, a Dirichlet-multinomial model is implemented.
-    External designs incorporate historical data through power priors
-    using exact conjugate representations (Normal-Inverse-Chi-squared for single
-    continuous, Normal-Inverse-Wishart for two continuous, and Dirichlet for
-    binary endpoints), enabling closed-form posterior computation without Markov
-    chain Monte Carlo (MCMC) sampling. This approach significantly reduces
-    computational burden while preserving complete Bayesian rigor. The package
-    also provides grid-search functions to find optimal Go and NoGo thresholds
-    that satisfy user-specified operating characteristic criteria for all
-    supported endpoint types and study designs. S3 print() and plot() methods
-    are provided for all decision probability classes, enabling formatted display
-    and visualisation of Go/NoGo/Gray operating characteristics across treatment
-    scenarios.
-    See Kang, Yamaguchi, and Han (2026) <doi:10.1080/10543406.2026.2655410>
-    for the methodological framework.
+Description: Bayesian quantitative decision-making for proof-of-concept
+    clinical trials with Go, NoGo and Gray decisions. A study is specified by
+    its sample sizes, conjugate prior distributions, external data borrowed
+    through power priors, a concurrent, external, hypothetical or fixed
+    control group, and a decision criterion based on the posterior or
+    posterior predictive probability of the treatment effect. The package
+    computes the decision for observed data, the operating characteristics
+    of a design under scenarios for the true parameters, the decision
+    thresholds that control the probabilities of false Go and false NoGo
+    decisions, and the decision boundaries over possible observed data. One
+    or two binary endpoints (Beta-binomial and Dirichlet-multinomial
+    models), one or two continuous endpoints (Normal-Inverse-chi-squared and
+    Normal-Inverse-Wishart models) and one time-to-event endpoint evaluated
+    by the milestone survival probability (exponential model with Gamma
+    priors) are supported. The posterior distributions have closed forms, so
+    Markov chain Monte Carlo (MCMC) sampling is not needed; the
+    probabilities are computed by exact summation, numerical integration, a
+    moment-matching approximation or Monte Carlo simulation, with the main
+    computations in C++. See Kang, Yamaguchi, and Han (2026)
+    <doi:10.1080/10543406.2026.2655410> for the methodological framework.
 License: GPL (>= 2)
 Encoding: UTF-8
 Language: en-US
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.3
 Imports:
     ggplot2 (>= 3.4.0),
-    gridExtra,
-    mvtnorm,
+    grDevices,
+    Rcpp,
     stats
+LinkingTo:
+    Rcpp
 Suggests:
-    testthat (>= 3.0.0),
     knitr,
     rmarkdown,
-    dplyr,
-    tidyr,
-    purrr,
-    spelling
+    spelling,
+    testthat (>= 3.0.0)
 VignetteBuilder: knitr
+Config/testthat/edition: 3
 URL: https://gosukehommaEX.github.io/BayesianQDM/, https://github.com/gosukehommaEX/BayesianQDM
 BugReports: https://github.com/gosukehommaEX/BayesianQDM/issues
+Config/roxygen2/version: 8.0.0