R Observatory: Metrics for iTOP version 1.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

iTOP

1.0.2Package record

Inferring the Topology of Omics Data

0packages depend

2.6Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Nanne AbenCRAN page ↗

Infers a topology of relationships between different datasets, such as multi-omics and phenotypic data recorded on the same samples. We based this methodology on the RV coefficient (Robert & Escoufier, 1976, doi:10.2307/2347233), a measure of matrix correlation, which we have extended for partial matrix correlations and binary data (Aben et al., 2018, doi:10.1101/293993).

Changes in 1.0.2

Some slight changes to the vignette and adding support for using n x 1 matrices.

From NEWS.md in the release

Install

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

install.packages("iTOP", 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-itop

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-iTOP

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-iTOP

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

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Nanne Aben <nanne.aben@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Nanne",
                    family = "Aben",
                    role = c("aut", "cre"),
                    email = "nanne.aben@gmail.com")
as necessary.

CRAN check page ↗

Slowest check: 2.4 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE9 OK, 5 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.2

READMENoVignettesYes · 1 · dynamicNEWSYes · 67% structured · mentions 1.0.2Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 16
Examples that run: 100%14 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

A quick introduction to iTOP HTML

How these are measured

Downloads

2.6K

CRAN downloads in the past year

Rank #14,514 · ~7/day · ~214/mo

Releases R versions

Daily download trend is not available in this view yet.

37430 days

83290 days

2.6K1 year

Compare downloads with other packages →

Also on65 r2u4 autocran

How downloads are counted

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing iTOP adds 1 package (0 with compiled code, 22 KB of source tarballs). Heaviest: corpcor 22 KB.

Depends (0)

none

Imports (2)

Matrixcorpcor

LinkingTo (0)

none

Suggests (5)

knitr rmarkdown NMF pcalg Rgraphviz

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (from the free-text Author field) (1)

Nanne Aben

Maintainer since 1.0.0 (2018)

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
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.0.2Latest
record
2018-06-13 · current release · diff ↗
R
R 3.5.0 released · 2018-04-23
1.0.1
record
2018-04-04 · diff ↗
1.0.0
record
2018-03-22
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2018-03-22
Total releases: 3 / 8 yrs
License: GPL-2 OSI
Download size: 47 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("iTOP")

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 iTOP version 1.0.2 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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