SMAHP

0.0.5

Survival Mediation Analysis of High-Dimensional Proteogenomic Data

0packages depend

2.2Kdownloads / year

42.9%test coverage

12/13checks pass

Overview

About

Maintained by Weijia FuFirst published 2025-03-241 releasesCRAN page ↗

SMAHP (pronounced as SOO-MAP) is a novel multi-omics framework for causal mediation analysis of high-dimensional proteogenomic data with survival outcomes. The full methodological details can be found in our recent preprint by Ahn S et al. (2025) doi:10.48550/arXiv.2503.08606.

Install

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

install.packages("SMAHP", 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-smahp

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-SMAHP

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-SMAHP

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 10.1 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.05

42.9%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 18%
Documented parameters: 98%
Return-value docs: 100%
References docs: 0%

Downloads

2.2K

CRAN downloads in the past year

Rank #22,357 · ~6/day · ~185/mo

Releases R versions

Daily download trend is not available in this view yet.

14930 days

48390 days

2.2K1 year

Compare downloads with other packages →

Also on91 r2u3 autocran

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (7)

data.table fdrtool ncvreg penAFTsurvivalstatsglmnet

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Weijia Fu

Maintainer, Author

Authors (2)

Weijia Fu

Maintainer, Author

Seungjun Ahn

Author

Contributors (1)

Zhigang Li

Contributor

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.0.5Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-03-24
Total releases: 1 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 93 KB / 1 file
Download size: 113 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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