Changelog

Source: NEWS.md

ipd 0.1.3

CRAN release: 2024-12-03

• Added a NEWS.md file to track changes to the package.

• Added a pkgdown site for the package.

• ipd() now allows for regression through the origin with intercept = FALSE argument.

• ipd() now takes an additional argument, na_action, to handle missing covariate data.

  • Currently supports "na.fail" and "na.omit". Defaults to na.fail.

  • Provides a more informative error message and lists which covariates are missing observations.

• ipd() now takes an additional argument, n_t, which denotes the (optional) size of the training set used to generate the prediction rule. Defaults to Inf but is necessary for the postpi_X methods if n_t < n, N, the number of labeled and unlabeled observations, respectively, in the data being analyzed.

ipd 0.1.4

CRAN release: 2025-01-07

• Added a help topic for the package itself (man/ipd-package.Rd) via R/ipd-package.R and roxygen2

• Updated the documentation for ipd():

  • Provided a more explicit description of the model argument, which is meant to specify the downstream inferential model or parameter to be estimated.

  • Clarified that not all columns in data are used in prediction unless explicitly referenced in the formula argument or in the label argument if the data are passed as one stacked data frame.

• Updated the documentation for simdat() to include a more thorough explanation of how to simulate data with this function.

• simdat() now outputs a data.frame with a column named "set_label" instead of "set" to denote the labeled/unlabeled observation indicator.

ipd 0.99.0

Summary:

• Preparations to archive on CRAN and move to Bioconductor.

• Slight formatting changes to conform to styler and lintr suggestions.

• Added PPIa, Chen and Chen methods from Gronsbell et al. (2025) “Another look at inference after prediction.”

Specific Changes:

• Version bump
  • Pre‑release version set to 0.99.0 for Bioconductor devel.
• DESCRIPTION updates
  • Depends: R (>= 4.4.0)
    
  • Added biocViews: Software
    
  • Added Suggests: BiocStyle, BiocManager
• Vignettes
  • Converted existing R Markdown vignettes to Bioconductor style with BiocStyle::html_document and proper VignetteIndexEntry headers.
  • Added examples for Chen and Chen, PPI “All” methods.
• NEWS & CITATION
  • Added NEWS.md entry (this file) and a CITATION file for package citation metadata.
• Testing & QA
  • Passed BiocCheck with no errors or warnings.
    
  • Updated testthat suite as needed for Bioc compliance.
• Continuous Integration
  • Added GitHub Actions via usethis::use_github_action("bioc-workflow") to run Bioconductor checks on Linux, macOS, and Windows.
• README

  • Installation instructions updated to:

    if (!requireNamespace("BiocManager", quietly=TRUE))
      install.packages("BiocManager")
    BiocManager::install("ipd")

  • Replaced CRAN build badge with:

    [![Bioc build status](https://bioconductor.org/shields/build/release/bioc/ipd.svg)](https://bioconductor.org/packages/ipd)

• New functions
  • ppi_a_ols() — implements the PPIa estimator for prediction‑powered inference.
    
  • chen_ols() — implements the Chen & Chen estimator for inference on predicted data.
  • .parse_inputs() - helper to validate and split input data.
  • .drop_unused_levels() - helper to drop unused factor levels and report which were removed.
  • .warn_differing_levels() - helper to warn on differing factor levels between labeled and unlabeled data.
  • .build_design() - helper to build design matrices and outcome vectors.
  • show() - implements S4 method for ipd class.
• Updates to functions
  • ipd() - registered new methods in wrapper.
  • ipd() - helper functions for parsing inputs and additional warnings to users when parsing formulas.
  • methods.R - Updated with new S4 class for ipd.
• Bioconductor submission prep
  • Branch created, tag v0.99.0 applied.
    
  • Will request CRAN archiving of the CRAN version upon successful Bioconductor acceptance.