initial commit public version

.Rbuildignore

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+^renv$
+^renv\.lock$
+^data-raw$
+^.*\.Rproj$
+^\.Rproj\.user$
+^LICENSE\.md$
+^codecov\.yml$
+^\.github$
+_\.new\.png$
+^\.\.$
+^deploy$
+^deploy_renv$
+^doc$
+^docs$
+^dev$
+^Meta$

.Rprofile

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+source("renv/activate.R")

.github/.gitignore

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+*.html

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

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+# 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, dev]
+  pull_request:
+    branches: [main, dev]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ubuntu-latest
+    env:
+      RENV_PROFILE: "dev"
+      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: '4.3.1'
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-tinytex@v2
+      - run: tlmgr --version
+
+      - 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")'

.github/workflows/test-coverage.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, dev]
+  pull_request:
+    branches: [main, dev]
+  workflow_dispatch:
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      RENV_PROFILE: "dev"
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      RENV_CONFIG_SANDBOX_ENABLED: false
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+          r-version: '4.3.1'
+
+      - uses: r-lib/actions/setup-tinytex@v2
+      - run: tlmgr --version    
+
+      - uses: r-lib/actions/setup-renv@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          packages: any::covr
+          needs: coverage 
+
+      - name: Install clinsight
+        shell: bash
+        run: R CMD INSTALL --preclean .
+
+      - name: Test coverage
+        run: covr::codecov(
+           quiet = FALSE,
+           clean = FALSE,
+           install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package"),
+           token = Sys.getenv("CODECOV_TOKEN")
+           )
+        shell: Rscript {0}
+
+      - 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@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+*.html
+*.tmp
+~$*
+docs/*
+# {shinytest2}: Ignore new debug snapshots for `$expect_values()`
+*_.new.png
+inst/doc
+/doc/
+/Meta/
+*.sqlite

DESCRIPTION

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+Package: clinsight
+Title: ClinSight
+Version: 0.0.0.9000
+Authors@R: c(
+    person("Leonard Daniël", "Samson", , "[email protected]", role = c("cre", "aut")),
+    person("GCP-Service International Ltd.& Co. KG", role = "fnd")
+  )
+Description: Interactive application to monitor patient safety during
+    clinical trials. Goal is to provide an interactive overview of a
+    patients' data, highlighting not yet reviewed data, and to improve
+    assessments of the patients' safety. Secondary goal is to improve data
+    quality by identifying suspicious outliers.
+License: Apache License (>= 2) | file LICENSE
+URL: https://github.com/LDSamson/clinsight
+BugReports: https://github.com/LDSamson/clinsight/issues
+Depends: 
+    R (>= 4.1)
+Imports: 
+    bslib,
+    config,
+    DBI,
+    dbplyr (>= 2.4.0),
+    dplyr,
+    DT,
+    ggplot2,
+    golem,
+    htmltools,
+    plotly,
+    readxl,
+    rlang,
+    rmarkdown,
+    RSQLite,
+    shiny,
+    shinycssloaders,
+    shinyjs,
+    shinymanager,
+    shinyWidgets,
+    stats,
+    tidyr,
+    timevis,
+    tools,
+    vroom,
+    withr
+Suggests: 
+    kableExtra,
+    knitr,
+    purrr,
+    shinytest2,
+    stringr,
+    testthat (>= 3.0.0)
+VignetteBuilder: 
+    knitr
+Config/renv/profiles/dev/dependencies: pkgdown, stringr, kableExtra,
+    usethis, cowplot
+Config/testthat/edition: 3
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3

LICENSE

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+YEAR: 2024
+COPYRIGHT HOLDER: clinsight authors