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twoPhaseSens: Sensitivity Analysis for Covariates Observed in Two-Phase Samples

Provides a structured method-comparison sensitivity-analysis workflow for linear regression when important continuous adjustment covariates are observed only in a Phase-2 subsample. Implements naive analysis, complete-case analysis, fully conditional specification multiple imputation, joint-model multiple imputation, inverse probability weighting, and augmented inverse probability weighting, with standardized tables, diagnostics, and publication-style forest plots. Methodological background is provided by Little and Rubin (2019) <doi:10.1002/9781119482260> for general missing-data methods, White and Carlin (2010) <doi:10.1002/sim.3944> for complete-case analysis with missing covariates, White, Royston and Wood (2011) <doi:10.1002/sim.4067> and van Buuren and Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03> for chained-equations multiple imputation, Quartagno, Grund and Carpenter (2019) <doi:10.32614/RJ-2019-028> for joint-model multiple imputation, Robins, Rotnitzky and Zhao (1994) <doi:10.1080/01621459.1994.10476818> for inverse-probability weighting with missing regressors, and Bang and Robins (2005) <doi:10.1111/j.1541-0420.2005.00377.x> for doubly robust estimation.

Version: 0.1.0
Imports: ggplot2, gtsummary (≥ 2.0.0), jomo, mice, rlang, tidyselect
Suggests: knitr, rmarkdown, testthat (≥ 3.0.0)
Published: 2026-10-22
DOI: 10.32614/CRAN.package.twoPhaseSens (may not be active yet)
Author: Rophence Ojiambo ORCID iD [aut, cre], Jemar Bather ORCID iD [aut]
Maintainer: Rophence Ojiambo <rophence.ojiambo at nyu.edu>
BugReports: https://github.com/rophenceojiambo/twoPhaseSens/issues
License: MIT + file LICENSE
URL: https://rophenceojiambo.github.io/twoPhaseSens/, https://github.com/rophenceojiambo/twoPhaseSens
NeedsCompilation: no
Materials: README, NEWS
CRAN checks: twoPhaseSens results

Documentation:

Reference manual: twoPhaseSens.html , twoPhaseSens.pdf
Vignettes: Getting started with twoPhaseSens (source, R code)

Downloads:

Package source: twoPhaseSens_0.1.0.tar.gz
Windows binaries: r-devel: not available, r-release: not available, r-oldrel: twoPhaseSens_0.1.0.zip
macOS binaries: r-release (arm64): twoPhaseSens_0.1.0.tgz, r-oldrel (arm64): twoPhaseSens_0.1.0.tgz, r-release (x86_64): twoPhaseSens_0.1.0.tgz, r-oldrel (x86_64): twoPhaseSens_0.1.0.tgz

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.