R Observatory: Metrics for fusedTree version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

fusedTree

1.1.0Package record

Fused Partitioned Regression for Clinical and Omics Data

0packages depend

5.5Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Jeroen M. GoedhartCRAN page ↗Declared funder: Hanarth Fonds

Fit (generalized) linear regression models in each leaf node of a tree. The tree is constructed using clinical variables only. The linear regression models are constructed using (high-dimensional) omics variables only. The leaf-node-specific regression models are estimated using the penalized likelihood including a standard ridge (L2) penalty and a fusion penalty that links the leaf-node-specific regression models to one another. The intercepts of the leaf nodes reflect the effects of the clinical variables and are left unpenalized. The tree, fitted with the clinical variables only, should be constructed outside of the package with the 'rpart' 'R' package. See Goedhart and others (2024) doi:10.48550/arXiv.2411.02396 for details on the method.

Changes in 1.1.0

New features

Tree fits are now also accepted from from the partykit package

(constparty objects), instead of only from the rpart package.

Functions fusedTree and PenOpt now take a new optional input argument

symFusion. Setting this argument to FALSE allows for asymmetric fusion,

where omics effects in nodes having similar predictions of the response

(using only clinical variables) will be shrunken less toward each other compared

to omics effects in nodes having more distinct predictions.

For memory efficiency, Matrix algebra is now conduced using sparse matrices

from the Matrix package when X is high-dimensional.

Predict function does not require the test response by default anymore. Rather,

it is an optional parameter.

From NEWS.md in the release

Install

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

install.packages("fusedTree", 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-fusedtree

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-fusedTree

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-fusedTree

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: 1.0 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.0

READMEYes · 771 wordsVignettesNoNEWSYes · 100% structured · mentions 1.1.0Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 5
Examples that run: 100%5 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 40%

How these are measured

Downloads

5.5K

CRAN downloads in the past year

Rank #12,888 · ~15/day · ~457/mo

Releases R versions

Daily download trend is not available in this view yet.

33830 days

87190 days

5.5K1 year

Compare downloads with other packages →

Also on54 r2u3 autocran

How downloads are counted

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Installing fusedTree adds 10 packages (5 with compiled code, 6.9 MB of source tarballs). Heaviest: partykit 2.1 MB, sandwich 1.4 MB, mvtnorm 1.0 MB.

Depends (0)

none

Imports (5)

MatrixsplitToolssurvivaltreeClust partykit

LinkingTo (0)

none

Suggests (1)

rpart

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (5)

Jeroen M. Goedhart

Wessel N. van Wieringen

Author

Author of 'porridge' 'R' package, from which many functionalities have been adopted

Hanarth Fonds

Funder

Thomas Klausch

Thesis advisor

Mark A. van de Wiel

Thesis advisor

Listed in earlier versions (3)

Show 3 peopleHide 3 people

Mark A.

no longer listed · 1.0.1 to 1.1.0

Jeroen M.

no longer listed · 1.0.1 to 1.1.0

Wessel N.

no longer listed · 1.0.1 to 1.1.0

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.1.0Latest
record
2025-08-20 · current release · diff ↗
1.0.1
record
2025-07-11
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-07-11
Total releases: 2 / 1 yrs
License: GPL (>= 3) OSI
Download size: 43 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("fusedTree")

Format

Goedhart, J. M., Hanarth Fonds, Klausch, T., van Wieringen, W. N., & van de Wiel, M. A. (2025). fusedTree: Fused Partitioned Regression for Clinical and Omics Data (Version 1.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.fusedTree

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 fusedTree version 1.1.0 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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