R Observatory: Metrics for asmbPLS version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

asmbPLS

1.0.0

Predicting and Classifying Patient Phenotypes with Multi-Omics Data

0packages depend

3.4Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Runzhi ZhangFirst published 2023-04-171 releasesCRAN page ↗

Adaptive Sparse Multi-block Partial Least Square, a supervised algorithm, is an extension of the Sparse Multi-block Partial Least Square, which allows different quantiles to be used in different blocks of different partial least square components to decide the proportion of features to be retained. The best combinations of quantiles can be chosen from a set of user-defined quantiles combinations by cross-validation. By doing this, it enables us to do the feature selection for different blocks, and the selected features can then be further used to predict the outcome. For example, in biomedical applications, clinical covariates plus different types of omics data such as microbiome, metabolome, mRNA data, methylation data, copy number variation data might be predictive for patients outcome such as survival time or response to therapy. Different types of data could be put in different blocks and along with survival time to fit the model. The fitted model can then be used to predict the survival for the new samples with the corresponding clinical covariates and omics data. In addition, Adaptive Sparse Multi-block Partial Least Square Discriminant Analysis is also included, which extends Adaptive Sparse Multi-block Partial Least Square for classifying the categorical outcome.

Install

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

install.packages("asmbPLS", 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-asmbpls

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-asmbPLS

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-asmbPLS

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

Health

CRAN checks

13OK

Slowest check: 8.9 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

4

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 3 earlier snapshots

NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 296 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 6%

Downloads

3.4K

CRAN downloads in the past year

Rank #10,340 · ~9/day · ~284/mo

Releases R versions

Daily download trend is not available in this view yet.

28930 days

92590 days

3.4K1 year

Compare downloads with other packages →

Also on409 r2u39 autocran

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (4)

Rcpp ggplot2 ggpubrstats

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Runzhi Zhang

Author, Maintainer

Authors (2)

Runzhi Zhang

Author, Maintainer

Susmita Datta

Author, Thesis advisor

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2023-04-17
Total releases: 1 / 3 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 1.1 MB / 2 files
Download size: 1.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("asmbPLS")

Format

Zhang, R., & Datta, S. (2023). asmbPLS: Predicting and Classifying Patient Phenotypes with Multi-Omics Data (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.asmbPLS

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 asmbPLS version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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