R Observatory: Metrics for SurrogateRegression version 0.6.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SurrogateRegression

0.6.0.1Package record

Surrogate Outcome Regression Analysis

0packages depend

3Kdownloads / year

92.2%test coverage

13/13flavors OK

Overview

About

Maintained by Zachary McCawCRAN page ↗

Performs estimation and inference on a partially missing target outcome (e.g. gene expression in an inaccessible tissue) while borrowing information from a correlated surrogate outcome (e.g. gene expression in an accessible tissue). Rather than regarding the surrogate outcome as a proxy for the target outcome, this package jointly models the target and surrogate outcomes within a bivariate regression framework. Unobserved values of either outcome are treated as missing data. In contrast to imputation-based inference, no assumptions are required regarding the relationship between the target and surrogate outcomes. Estimation in the presence of bilateral outcome missingness is performed via an expectation conditional maximization either algorithm. In the case of unilateral target missingness, estimation is performed using an accelerated least squares procedure. A flexible association test is provided for evaluating hypotheses about the target regression parameters. For additional details, see: McCaw ZR, Gaynor SM, Sun R, Lin X: "Leveraging a surrogate outcome to improve inference on a partially missing target outcome" doi:10.1111/biom.13629.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("SurrogateRegression", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-surrogateregression

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-SurrogateRegression

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-SurrogateRegression

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 3.5 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.6.0.1

READMENoVignettesYes · 1 · staticNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 38includes a package overview page
Examples that run: 50%2 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Surrogate Outcome Regression Analysis PDF

How these are measured

Downloads

3K

CRAN downloads in the past year

Rank #14,135 · ~8/day · ~251/mo

Releases R versions

Daily download trend is not available in this view yet.

29330 days

82590 days

3K1 year

Compare downloads with other packages →

Also on375 r2u8 autocran47 c2d4u

How downloads are counted

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing SurrogateRegression adds 2 packages (2 with compiled code, 2.8 MB of source tarballs). Heaviest: Rcpp 1.8 MB, RcppArmadillo 1.0 MB.

Depends (1)

R >= 3.4.0

Imports (3)

methodsRcppstats

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (4)

testthat knitr rmarkdown withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (1)

Zachary McCaw

Author, Maintainer since 0.5.0 (2020)

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.6.0.1Latest
record
2023-10-01 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
0.6.0
record
2022-08-05 · diff ↗ ·
removed 7 exports
Fit.BNEM, Fit.BNLS, Fit.BNR, Score.BNEM, Test.BNR, Wald.BNEM, Wald.BNLS

added 2 exports
FitBNR, TestBNR
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.5.0
record
2020-12-03
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-12-03
Total releases: 3 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.4.0
Download size: 449 KB

Appears in task views

Missing Data Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SurrogateRegression")

Format

McCaw, Z. (2023). SurrogateRegression: Surrogate Outcome Regression Analysis (Version 0.6.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.SurrogateRegression

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for SurrogateRegression version 0.6.0.1 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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