Initial commit

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$
+^LICENSE\.md$

.gitattributes

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+# Auto detect text files and perform LF normalization
+* text=auto

.github/.gitignore

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+*.html
+*-tmp.yaml
+depends.Rds
+R-version

.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, master, devel]
+  pull_request:
+    branches: [main, master, devel]
+  schedule:
+    # (see https://crontab.guru)
+    - cron: "30 3 * */2 TUE"
+  workflow_dispatch:
+
+name: R-CMD-check
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    concurrency:
+      group: >
+        ${{ github.workflow }}-${{ matrix.config.os }}-${{ matrix.config.r }})-
+        ${{ github.event_name != 'pull_request' || github.run_id }}
+      cancel-in-progress: true
+
+    name: ${{ matrix.config.os }} (R-${{ 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:
+      R_KEEP_PKG_SOURCE: yes
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          use-public-rspm: true
+          extra-repositories: "https://mokymai.github.io/download/"
+
+      - 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

.github/workflows/drat--publish-package.yaml

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+on:
+  push:
+    branches: [master, main]
+  workflow_dispatch:
+
+name: Publish package (drat)
+
+jobs:
+  drat:
+    runs-on: ${{ matrix.config.os }}
+
+    name: "drat: ${{ matrix.config.os }} (R-${{ matrix.config.r }})"
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+          - {os: windows-latest, r: 'oldrel'}
+          - {os: macOS-latest,   r: 'release'}
+          - {os: macOS-latest,   r: 'oldrel'}
+          # - {os: windows-latest, r: 'devel'}
+          # - {os: macOS-latest,   r: 'devel'}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      GITHUB_PAT:  ${{ secrets.GITHUB_TOKEN }}
+      SOURCE_REPO: ${{ github.repository }}
+      DEST_REPO:   mokymai/download
+      TMP_DIR:     tmp_dir
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Info
+        run: |
+          echo "GitHub actor: ${{ github.actor }}"
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          use-public-rspm: true
+          extra-repositories: "https://mokymai.github.io/download/"
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 1
+          extra-packages: |
+            roxygen2
+            devtools
+            drat
+
+      - name: Roxygenize
+        shell: Rscript {0}
+        run:   roxygen2::roxygenize()
+
+      - name: Build source package
+        if: runner.os == 'Windows' && matrix.config.r == 'release'
+        shell: Rscript {0}
+        run: |
+          dir.create("check", showWarnings = FALSE)
+          devtools::build(path = "check")
+
+      - name: Build binary package
+        if: runner.os != 'Linux'
+        shell: Rscript {0}
+        run: |
+            dir.create("check", showWarnings = FALSE)
+            devtools::build(path = "check", binary = TRUE)
+
+# The steps to include the built package in ${DEST_REPO}
+      - name: Configure Git
+        run: |
+          git config --global user.email "[email protected]"
+          git config --global user.name  "GitHub Actions | ${{ github.event.repository.name }}"
+          # git config --global url."https://${TOKEN}:[email protected]/".insteadOf "https://github.com/"
+        env:
+          TOKEN: ${{ secrets.DEPLOY_DRAT_TOKEN }}
+
+      - name: Git clone DEST_REPO
+        uses: actions/checkout@v3
+        with:
+          repository: ${{ env.DEST_REPO }} # 'mokymai/download'
+          ref:   'master'
+          path:  "${{ env.TMP_DIR }}"
+          token: "${{ secrets.DEPLOY_DRAT_TOKEN }}"
+
+      - name: Drat -- insert
+        if: success()
+        shell: Rscript {0}
+        run: |
+          built_packages <-
+            list.files(
+              path       = "check",
+              pattern    = "[.]tar[.]gz$|[.]tgz$|[.]zip$",
+              full.names = TRUE
+            )
+
+          built_packages
+
+          for (i in seq_along(built_packages)) {
+            drat::insertPackages(
+              file    = built_packages[i],
+              repodir = Sys.getenv("TMP_DIR"),
+              action  = "archive"
+            )
+          }
+
+      - name: Drat -- commit and push
+        if: success()
+        shell: bash
+        run: |
+          cd "${TMP_DIR}" # move into the subdir, which is Git controlled
+          git add *
+          git add -f *.tar.gz
+          git commit -m "Update from ${SOURCE_REPO} ${{ runner.os }} R-${{ matrix.config.r }}" || echo "Nothing to commit"
+          git push origin master || echo "Nothing to commit"
+

.github/workflows/pkgdown.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, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: Update website (pkgdown)
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: "release"
+          use-public-rspm: true
+          extra-repositories: "https://mokymai.github.io/download/"
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, any::devtools, local::.
+          needs: website
+
+      - name: Configure Git
+        run: |
+           git config --global user.email "[email protected]"
+           git config --global user.name  "GitHub Actions"
+
+      - name: Update Rd files
+        run: |
+          devtools::document(roclets = c('rd', 'collate', 'namespace'))
+        shell: Rscript {0}
+
+      - name: Commit documentation updates (if any)
+        run: |
+          git add --all
+          git commit -m 'Re-build documentation' || echo "No changes to commit"
+          git push origin || echo "No changes to commit (documentation)"
+
+      - name: Render README
+        run: Rscript -e 'rmarkdown::render("README.Rmd")'
+
+      - name: Commit README (if changed)
+        run: |
+           git commit README.md -m 'Re-build README.Rmd before pkgdown' || echo "No changes to commit (README)"
+           git push origin || echo "No changes to commit (README)"
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

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+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+.RDataTmp
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+
+# pkgdown site
+docs/
+
+# translation temp files
+po/*~
+
+# RStudio Connect folder
+rsconnect/

DESCRIPTION

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+Package: pi
+Type: Package
+Title: Confidence Intervals (CI) / Pasikliautinieji Intervalai (PI)
+Version: 0.0.1
+Authors@R: 
+    person("Vilmantas", "Gegzna", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0002-9500-5167"),
+           email = "[email protected]"
+    )
+Description: Patogumo funkcijos, skirtos skaičiuoti pasikliautinuosius intervalus.
+License: MIT + file LICENSE
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2
+Imports:
+  DescTools,
+  dplyr,
+  tidyr,
+  purrr,
+  forcats,
+  tibble,
+  checkmate

LICENSE

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+YEAR: 2024
+COPYRIGHT HOLDER: Vilmantas Gegzna

LICENSE.md

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+# MIT License
+
+Copyright (c) 2024 Vilmantas Gegzna
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(ci_binom)
+export(ci_boot)
+export(ci_mean_t)
+export(ci_mean_t_stat)
+export(ci_multinom)
+importFrom(stats,qt)
+importFrom(utils,data)