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Merge pull request #7 from abichat/dev
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‎.github/workflows/R-CMD-check-dev.yaml

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches:
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- dev
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pull_request:
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branches:
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- dev
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jobs:
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R-CMD-check:
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if: "!contains(github.event.head_commit.message, 'skip ci')"
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runs-on: macOS-latest
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-r@master
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- name: Install dependencies
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run: |
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install.packages(c("remotes", "rcmdcheck"))
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remotes::install_deps(dependencies = TRUE)
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shell: Rscript {0}
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- name: Check
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run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
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shell: Rscript {0}
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::rcmdcheck
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needs: check
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- uses: r-lib/actions/check-r-package@v2

‎.github/workflows/R-CMD-check.yaml

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches:
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- master
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pull_request:
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branches:
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- master
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- dev
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name: R-CMD-check
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jobs:
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R-CMD-check:
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if: "!contains(github.event.head_commit.message, 'skip ci')"
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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fail-fast: false
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matrix:
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config:
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- {os: macOS-latest, r: 'release'}
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- {os: windows-latest, r: 'release'}
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- {os: macOS-latest, r: 'release'}
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- {os: macOS-latest, r: 'devel'}
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- {os: ubuntu-16.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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- {os: ubuntu-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'oldrel-1'}
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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RSPM: ${{ matrix.config.rspm }}
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-r@master
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- uses: r-lib/actions/setup-pandoc@master
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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shell: Rscript {0}
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- name: Cache R packages
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if: runner.os != 'Windows'
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uses: actions/cache@v1
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
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- name: Install system dependencies
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if: runner.os == 'Linux'
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env:
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RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
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run: |
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Rscript -e "remotes::install_github('r-hub/sysreqs')"
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sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
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sudo -s eval "$sysreqs"
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- name: Install dependencies
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run: |
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remotes::install_deps(dependencies = TRUE)
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remotes::install_cran("rcmdcheck")
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shell: Rscript {0}
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- name: Check
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env:
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_R_CHECK_CRAN_INCOMING_REMOTE_: false
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run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
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shell: Rscript {0}
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extra-packages: any::rcmdcheck
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needs: check
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- name: Upload check results
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if: failure()
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uses: actions/upload-artifact@master
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- uses: r-lib/actions/check-r-package@v2
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with:
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name: ${{ runner.os }}-r${{ matrix.config.r }}-results
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path: check
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upload-snapshots: true

‎.github/workflows/pkgdown.yaml

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: master
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pull_request:
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branches: [main, master]
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release:
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types: [published]
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workflow_dispatch:
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name: pkgdown
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jobs:
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pkgdown:
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runs-on: macOS-latest
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runs-on: ubuntu-latest
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# Only restrict concurrency for non-PR jobs
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concurrency:
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group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
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env:
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GITHUB_PAT: ${{ secrets.GH_TOKEN }}
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steps:
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-r@master
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-pandoc@master
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), "depends.Rds", version = 2)
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shell: Rscript {0}
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- name: Cache R packages
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uses: actions/cache@v1
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: macOS-r-3.6-${{ hashFiles('depends.Rds') }}
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restore-keys: macOS-r-3.6-
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extra-packages: any::pkgdown, local::.
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needs: website
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- name: Install dependencies
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run: |
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install.packages("remotes")
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remotes::install_deps(dependencies = TRUE)
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remotes::install_dev("pkgdown")
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- name: Build site
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run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
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shell: Rscript {0}
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- name: Install package
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run: R CMD INSTALL .
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- name: Deploy package
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run: pkgdown::deploy_to_branch(new_process = FALSE)
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shell: Rscript {0}
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- name: Deploy to GitHub pages 🚀
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if: github.event_name != 'pull_request'
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uses: JamesIves/[email protected]
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with:
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clean: false
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branch: gh-pages
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folder: docs

‎.gitignore

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.Rhistory
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.RData
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.Rproj.user
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.DS_Store

‎DESCRIPTION

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Package: evabic
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Title: Evaluation of Binary Classifiers
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Version: 0.0.4
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Version: 0.1.0
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Authors@R:
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person(given = "Antoine",
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family = "Bichat",
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role = c("aut", "cre"),
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email = "[email protected]",
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person("Antoine", "Bichat", , "[email protected]", role = c("aut", "cre"),
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comment = c(ORCID = "0000-0001-6599-7081"))
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Description: Evaluates the performance of binary classifiers.
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Computes confusion measures (TP, TN, FP, FN), derived measures (TPR,
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FDR, accuracy, F1, DOR, ..), and area under the curve. Outputs are
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well suited for nested dataframes.
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Description: Evaluates the performance of binary classifiers. Computes
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confusion measures (TP, TN, FP, FN), derived measures (TPR, FDR,
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accuracy, F1, DOR, ..), and area under the curve. Outputs are well
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suited for nested dataframes.
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License: GPL-3
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URL: https://abichat.github.io/evabic,
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https://github.com/abichat/evabic
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URL: https://abichat.github.io/evabic, https://github.com/abichat/evabic
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BugReports: https://github.com/abichat/evabic/issues
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Suggests:
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testthat (>= 2.1.0)
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Encoding: UTF-8
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Language: en-US
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LazyData: true
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Roxygen: list(markdown = TRUE)
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RoxygenNote: 7.1.0
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RoxygenNote: 7.2.1

‎NEWS.md

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# evabic 0.1.0
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* Doc update to fix HTML5 issues for CRAN check.
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* Considered as stable.
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# evabic 0.0.4
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* Clear error message when using `nl2c()` with a unnamed logical vector.

‎R/measures.R

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#' Available measures in \code{evabic}
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#'
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#' @details
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#' \if{html}{\figure{confusionmatrix.png}{options: width="50\%" align="middle"}}
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#' \if{html}{\figure{confusionmatrix.png}{options: width="50\%"
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#' style="float:middle"}}
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#' \if{latex}{\figure{confusionmatrix.png}{options: width=15cm}}
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#' \describe{
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#' \item{TP}{True Positive}

‎README.Rmd

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)
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```
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# evabic <a href='https://abichat.github.io/evabic'><img src='man/figures/logo.png' align="right" height="139" /></a>
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# evabic <a href='https://abichat.github.io/evabic'><img src='man/figures/logo.png' style="float:right" height="139" /></a>
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```{r, echo = FALSE}
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version <- as.vector(read.dcf('DESCRIPTION')[, 'Version'])
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<!-- badges: start -->
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[![license](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html)
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[![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
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[![lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable)
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[![packageversion](https://img.shields.io/badge/package%20version-`r version`-orange.svg)](https://github.com/abichat/evabic/blob/master/DESCRIPTION)
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[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/evabic)](https://cran.r-project.org/package=evabic)
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[![Codecov test coverage](https://codecov.io/gh/abichat/evabic/branch/master/graph/badge.svg)](https://codecov.io/gh/abichat/evabic?branch=master)
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[![Codacy Badge](https://api.codacy.com/project/badge/Grade/c32dcc4c1c3f40a5950e1c10ea6dfb18)](https://www.codacy.com/app/abichat/evabic?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=abichat/evabic&amp;utm_campaign=Badge_Grade)
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[![R build status](https://github.com/abichat/evabic/workflows/R-CMD-check/badge.svg)](https://github.com/abichat/evabic/actions)
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[![R-CMD-check](https://github.com/abichat/evabic/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/abichat/evabic/actions/workflows/R-CMD-check.yaml)
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[![Documentation](https://img.shields.io/badge/documentation-pkgdown-E91E63.svg)](https://abichat.github.io/evabic/)
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[![last-commit](https://img.shields.io/github/last-commit/abichat/evabic.svg)](https://github.com/abichat/evabic/commits/master)
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<!-- badges: end -->

‎README.md

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<!-- README.md is generated from README.Rmd. Please edit that file -->
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# evabic <a href='https://abichat.github.io/evabic'><img src='man/figures/logo.png' align="right" height="139" /></a>
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# evabic <a href='https://abichat.github.io/evabic'><img src='man/figures/logo.png' style="float:right" height="139" /></a>
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<!-- badges: start -->
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[![license](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html)
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[![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
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[![packageversion](https://img.shields.io/badge/package%20version-0.0.4-orange.svg)](https://github.com/abichat/evabic/blob/master/DESCRIPTION)
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[![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/evabic)](https://cran.r-project.org/package=evabic)
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[![Codecov test
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coverage](https://codecov.io/gh/abichat/evabic/branch/master/graph/badge.svg)](https://codecov.io/gh/abichat/evabic?branch=master)
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[![Codacy
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Badge](https://api.codacy.com/project/badge/Grade/c32dcc4c1c3f40a5950e1c10ea6dfb18)](https://www.codacy.com/app/abichat/evabic?utm_source=github.com&utm_medium=referral&utm_content=abichat/evabic&utm_campaign=Badge_Grade)
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[![R build
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status](https://github.com/abichat/evabic/workflows/R-CMD-check/badge.svg)](https://github.com/abichat/evabic/actions)
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[![lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable)
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[![packageversion](https://img.shields.io/badge/package%20version-0.1.0-orange.svg)](https://github.com/abichat/evabic/blob/master/DESCRIPTION)
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[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/evabic)](https://cran.r-project.org/package=evabic)
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[![R-CMD-check](https://github.com/abichat/evabic/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/abichat/evabic/actions/workflows/R-CMD-check.yaml)
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[![Documentation](https://img.shields.io/badge/documentation-pkgdown-E91E63.svg)](https://abichat.github.io/evabic/)
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[![last-commit](https://img.shields.io/github/last-commit/abichat/evabic.svg)](https://github.com/abichat/evabic/commits/master)
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<!-- badges: end -->
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``` r
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evabic::ebc_allmeasures
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#> [1] "TP" "FP" "FN" "TN" "TPR" "TNR" "PPV" "NPV" "FNR" "FPR" "FDR" "FOR"
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#> [13] "ACC" "BACC" "F1" "PLR" "NLR" "DOR"
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#> [1] "TP" "FP" "FN" "TN" "TPR" "TNR" "PPV" "NPV" "FNR" "FPR" "FDR"
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#> [12] "FOR" "ACC" "BACC" "F1" "PLR" "NLR" "DOR"
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```
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All measures are computed from the confusion matrix:
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<center>
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<img src="man/figures/confusionmatrix.png" width="50%"/>
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</center>
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## Example
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#> F-statistic: 69.99 on 7 and 42 DF, p-value: < 2.2e-16
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pvalues <- summary(model)$coefficients[-1, 4]
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pvalues
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#> X1 X2 X3 X4 X5 X6 X7
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#> 0.004366456 0.829771754 0.003469737 0.491828466 0.581608670 0.887948400 0.449664443
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#> X1 X2 X3 X4 X5 X6
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#> 0.004366456 0.829771754 0.003469737 0.491828466 0.581608670 0.887948400
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#> X7
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#> 0.449664443
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detected_var <- names(pvalues[pvalues < 0.05])
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detected_var
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#> [1] "X1" "X3"
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With `ebc_tidy_by_threshold()`, you can ask for the evolution of
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measures according to a moving threshold if you provide the vector of
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p-values (or any
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score).
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p-values (or any score).
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``` r
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df_measures <- ebc_tidy_by_threshold(detection_values = pvalues, true = predictors, m = 7,
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#> 8 Inf 1.0000000 1.00 0.5714286 0.4285714 0.5000000 0.6000000
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```
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This makes it easy to plot various-threshold curves like ROC
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curve.
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This makes it easy to plot various-threshold curves like ROC curve.
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``` r
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plot(df_measures$FPR, df_measures$TPR, type = "b", xlab = "FPR", ylab = "TPR")

‎dev_history.R

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load_all()
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document()
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attachment::att_to_description()
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attachment::att_amend_desc()
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use_tidy_description()
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# covr::package_coverage()

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