R Observatory: Metrics for cuperdec version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

cuperdec

1.1.0Package record

Cumulative Percent Decay Curve Generator

0packages depend

3Kdownloads / year

78.7%test coverage

13/13flavors OK

Overview

About

Maintained by James A. Fellows YatesCRAN page ↗GitHub ↗Issues ↗

Calculates and visualises cumulative percent 'decay' curves, which are typically calculated from metagenomic taxonomic profiles. These can be used to estimate the level of expected 'endogenous' taxa at different abundance levels retrieved from metagenomic samples, when comparing to samples of known sampling site or source. Method described in Fellows Yates, J. A. et. al. (2021) Proceedings of the National Academy of Sciences USA doi:10.1073/pnas.2021655118.

Changes in 1.1.0

Added

Added full publication citation information for package
Added options to customise number of facets in grouped cuperdec plots

Updated

Updated vignette to include graphical visualisation of filter thresholds

Fixed

Fixed badly sized plots in vignette
Fixed missing validation when trying to filter pre-made curve files

From NEWS.md in the release

Install

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

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

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("jfy133/cuperdec")

Development version from jfy133/cuperdec. Installs pak first if it is not already available.

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-cuperdec

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-cuperdec

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-cuperdec

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: 2.7 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-10-20
ERROR12 OK, 1 ERROR2026-10-15
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 · 167 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.1.0Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 11
Examples that run: 100%11 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Introduction to cuperdec HTML

How these are measured

Downloads

3K

CRAN downloads in the past year

Rank #14,913 · ~8/day · ~250/mo

Releases R versions

Daily download trend is not available in this view yet.

27230 days

81490 days

3K1 year

Compare downloads with other packages →

Also on97 r2u12 autocran491 conda_forge

How downloads are counted

Repository

jfy133/cuperdec ↗Account: jfy133

4Stars

0Forks

1Open issues

0Open PRs

5Releases

91Commits

1Commit identities

91 commits · Last activity 2022-09-12 · 0% stars, 30d · Default branch at 1.1.0.9000, ahead of CRAN 1.1.0 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 76
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2025-05-20 · 42026-07-07 · 4

How these are measured

PracticesBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/jfy133/cuperdec on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on macOS

Coverage (1)

Coverage reporting (Codecov)

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing cuperdec adds 39 packages (20 with compiled code, 30 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, isoband 1.5 MB.

Depends (1)

R >= 3.5.0

Imports (6)

dplyr ggplot2 magrittr readr rlang tidyr

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown testthat tibble

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

James A. Fellows Yates

Author, Maintainer since 1.0.0 (2021)

Releases (2)

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
1.1.0Latest
record
2021-09-12 · current release · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.0
record
2021-04-07
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-04-07
Total releases: 2 / 5 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 206 KB / 3 files
Download size: 1.3 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("cuperdec")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1073/pnas.2021655118.

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 cuperdec version 1.1.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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