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Update email address and paper citations
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‎.github/workflows/R-CMD-check.yaml‎

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# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
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# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
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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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- main
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- master
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branches: [main, master]
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pull_request:
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branches:
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- main
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- master
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branches: [main, master]
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name: R-CMD-check
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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: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: windows-latest, r: 'release'}
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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_CHECK_FORCE_SUGGESTS_: false
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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: actions/checkout@v3
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- uses: r-lib/actions/setup-r@v1
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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: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- uses: r-lib/actions/setup-pandoc@v1
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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shell: Rscript {0}
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- name: Restore R package cache
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if: runner.os != 'Windows'
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uses: actions/cache@v2
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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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run: |
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while read -r cmd
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do
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eval sudo $cmd
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done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
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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: |
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options(crayon.enabled = TRUE)
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rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
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shell: Rscript {0}
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dependencies: '"hard"'
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extra-packages: any::rcmdcheck, any::covr, any::testthat
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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@main
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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/test-coverage.yaml‎

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This file was deleted.

‎DESCRIPTION‎

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Package: natstrat
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Type: Package
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Title: Obtain Unweighted Natural Strata that Balance Many Covariates
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Version: 2.0.0
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Authors@R: c(
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person("Katherine", "Brumberg", email = "kbrum@wharton.upenn.edu",
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role=c("aut", "cre")))
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Description: Natural strata can be used in observational studies to balance
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the distributions of many covariates across any number of treatment
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groups and any number of comparisons. These strata have proportional
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amounts of units within each stratum across the treatments, allowing
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for simple interpretation and aggregation across strata. Within each
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stratum, the units are chosen using randomized rounding of a linear
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program that balances many covariates.
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To solve the linear program, the 'Gurobi' commercial optimization software
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is recommended, but not required. The 'gurobi' R package can be installed following the instructions
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at <https://www.gurobi.com/documentation/9.1/refman/ins_the_r_package.html>.
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URL: https://github.com/kkbrum/natstrat, https://kkbrum.github.io/natstrat/, https://www.gurobi.com/documentation/9.1/refman/ins_the_r_package.html
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BugReports: https://github.com/kkbrum/natstrat/issues
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License: GPL-3
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Encoding: UTF-8
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LazyData: true
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RoxygenNote: 7.1.1
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Imports:
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Rglpk,
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stats,
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plyr,
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pps,
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sampling,
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ggplot2,
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rlang,
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ramify,
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slam
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Depends:
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R (>= 2.10),
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caret
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Suggests:
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knitr,
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rmarkdown,
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markdown,
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testthat (>= 3.0.0),
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DT,
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stringr,
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covr,
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gurobi
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VignetteBuilder: knitr
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Config/testthat/edition: 3
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Package: natstrat
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Type: Package
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Title: Obtain Unweighted Natural Strata that Balance Many Covariates
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Version: 2.0.1
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Authors@R: c(
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person("Katherine", "Brumberg", email = "kbrum@umich.edu",
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role=c("aut", "cre")))
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Description: Natural strata can be used in observational studies to balance
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the distributions of many covariates across any number of treatment
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groups and any number of comparisons. These strata have proportional
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amounts of units within each stratum across the treatments, allowing
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for simple interpretation and aggregation across strata. Within each
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stratum, the units are chosen using randomized rounding of a linear
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program that balances many covariates. For more details, see Brumberg et al. (2022) <https://doi.org/10.1111/rssa.12848> and Brumberg et al.(2023) <https://doi.org/10.1093/jrsssc/qlad010>.
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To solve the linear program, the 'Gurobi' commercial optimization software
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is recommended, but not required. The 'gurobi' R package can be installed by following the instructions at <https://docs.gurobi.com/projects/optimizer/en/current/reference/r/setup.html> after claiming your free academic license at <https://www.gurobi.com/academia/academic-program-and-licenses/>.
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URL: https://github.com/kkbrum/natstrat, https://kkbrum.github.io/natstrat/, https://docs.gurobi.com/projects/optimizer/en/current/reference/r/setup.html
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BugReports: https://github.com/kkbrum/natstrat/issues
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License: GPL-3
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Encoding: UTF-8
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LazyData: true
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RoxygenNote: 7.3.1
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Imports:
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Rglpk,
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stats,
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plyr,
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pps,
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sampling,
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ggplot2,
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rlang,
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ramify,
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slam
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Depends:
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R (>= 2.10),
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caret
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Suggests:
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knitr,
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rmarkdown,
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markdown,
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testthat (>= 3.0.0),
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DT,
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stringr,
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covr,
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gurobi
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VignetteBuilder: knitr
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Config/testthat/edition: 3

‎NEWS.md‎

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# natstrat 2.0.0 (2026-02-03)
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This patch updates the maintainer's email address and adds paper citations.
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# natstrat 2.0.0 (2021-10-12)
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This version adds several new functionalities:
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* `generate_constraints` now returns only standardized outputs, not centered. The centering
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now takes place within `optimize_controls` instead
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# natstrat 1.0.0 (2021-05-17)
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The first released version.

‎README.Rmd‎

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<!-- badges: start -->
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[![R-CMD-check](https://github.com/kkbrum/natstrat/workflows/R-CMD-check/badge.svg)](https://github.com/kkbrum/natstrat/actions)
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[![Codecov test coverage](https://codecov.io/gh/kkbrum/natstrat/branch/master/graph/badge.svg)](https://app.codecov.io/gh/kkbrum/natstrat?branch=master)
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<!-- badges: end -->
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Natural strata can be used in observational studies to balance

‎README.md‎

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<!-- badges: start -->
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[![R-CMD-check](https://github.com/kkbrum/natstrat/workflows/R-CMD-check/badge.svg)](https://github.com/kkbrum/natstrat/actions)
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[![Codecov test
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coverage](https://codecov.io/gh/kkbrum/natstrat/branch/master/graph/badge.svg)](https://app.codecov.io/gh/kkbrum/natstrat?branch=master)
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<!-- badges: end -->
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Natural strata can be used in observational studies to balance the

‎cran-comments.md‎

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## Updated package
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This is an update to an existing package. In this major version I have added
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additional functionality, which is almost entirely backwards compatible.
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This is a patch to update my email address. All other changes are just to get checks/tests running smoothly.
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## Test environments
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* local windows install, R 4.0.3
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* local windows install, R 4.1.1
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* ubuntu-20.04 release (on github actions)
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* ubuntu-20.04 devel (on github actions)
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* macOS-latest release (on github actions)
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* win-builder (devel and release)
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* local macOS install, R 4.2.2
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- macOS builder
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- win-builder (devel and release)
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- github actions:
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- {os: windows-latest, r: 'release'}
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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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## R CMD check results
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There were no ERRORs or WARNINGs on release or devel.
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Only in my local windows install, using version 4.0.3 of R,
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there is 1 WARNING:
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Warning: package 'ggplot2' was built under R version 4.0.5
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As my package does not rely heavily on ggplot2, there should not be any issues
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with users using my package with earlier versions of R. There do not seem
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to have been any ggplot2 changes that affect my package.
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There were no ERRORs or WARNINGs.
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There were the following NOTEs:
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‎inst/CITATION‎

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citHeader("To cite natstrat in publications use:")
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bibentry(bibtype = "Manual",
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title = "natstrat: Obtain Unweighted Natural Strata that Balance Many Covariates",
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author = person("Katherine", "Brumberg"),
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year = 2024,
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note = paste("R package version", packageVersion("natstrat")),
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url = "https://github.com/kkbrum/natstrat",
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textVersion = paste("Brumberg, K. (2024). natstrat: Obtain Unweighted Natural Strata that Balance Many Covariates. R package version", packageVersion("natstrat"), ". https://github.com/kkbrum/natstrat")
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)
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bibentry(bibtype = "Article",
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title = "Using Randomized Rounding of Linear Programs to Obtain Unweighted Natural Strata that Balance Many Covariates",
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author = c(
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person("Katherine", "Brumberg"),
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person("Dylan", "S", "Small"),
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person("Paul", "R", "Rosenbaum")
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),
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journal = "Journal of the Royal Statistical Society Series A: Statistics in Society",
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year = 2022,
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volume = 185,
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number = 4,
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pages = "1931-1951",
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doi = "10.1111/rssa.12848",
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url = "https://doi.org/10.1111/rssa.12848",
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textVersion = "Brumberg, K., Small, D. S., & Rosenbaum, P. R. (2022). Using Randomized Rounding of Linear Programs to Obtain Unweighted Natural Strata that Balance Many Covariates. Journal of the Royal Statistical Society Series A: Statistics in Society, 185(4), 1931-1951. https://doi.org/10.1111/rssa.12848"
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)
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bibentry(bibtype = "Article",
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title = "Using natural strata when examining unmeasured biases in an observational study of neurological side effects of antibiotics",
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author = c(
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person("Katherine", "Brumberg"),
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person("Darcy", "E", "Ellis"),
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person("Dylan", "S", "Small"),
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person("Sean", "Hennessy"),
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person("Paul", "R", "Rosenbaum")
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),
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journal = "Journal of the Royal Statistical Society Series C: Applied Statistics",
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year = 2023,
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volume = 72,
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number = 2,
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pages = "314-329",
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doi = "10.1093/jrsssc/qlad010",
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url = "https://doi.org/10.1093/jrsssc/qlad010",
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textVersion = "Brumberg, K., Ellis, D. E., Small, D. S., Hennessy, S., & Rosenbaum, P. R. (2023). Using natural strata when examining unmeasured biases in an observational study of neurological side effects of antibiotics. Journal of the Royal Statistical Society Series C: Applied Statistics, 72(2), 314-329. https://doi.org/10.1093/jrsssc/qlad010"
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)

‎man/natstrat-package.Rd‎

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