R Observatory: Metrics for cubfits version 0.1-4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

cubfits

0.1-4Package record

Codon Usage Bias Fits

0packages depend

8.4Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Wei-Chen ChenCRAN page ↗GitHub ↗Issues ↗

Estimating mutation and selection coefficients on synonymous codon bias usage based on models of ribosome overhead cost (ROC). Multinomial logistic regression and Markov Chain Monte Carlo are used to estimate and predict protein production rates with/without the presence of expressions and measurement errors. Work flows with examples for simulation, estimation and prediction processes are also provided with parallelization speedup. The whole framework is tested with yeast genome and gene expression data of Yassour, et al. (2009) doi:10.1073/pnas.0812841106.

Install

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

install.packages("cubfits", 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("snoweye/cubfits")

Development version from snoweye/cubfits. 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-cubfits

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-cubfits

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-cubfits

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: ‘Wei-Chen Chen <wccsnow@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

CRAN check page ↗

Slowest check: 3.4 min · r-devel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-06-09
ERROR11 OK, 1 NOTE, 1 ERROR2026-06-08
NOTE10 OK, 4 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1-4

READMEYes · 19 wordsVignettesYes · 1 · staticNEWSNoCitation fileYes · software entry onlyWebsitenot declared in DESCRIPTION

Help pages: 32 (2 internal)includes a package overview page
Examples that run: 0%29 never run
Exported functions with examples: 92%
Documented parameters: 97%
Return-value docs: 92%
Help pages citing references: 100%

Also includes 13 demo scripts (run with demo())

Vignettes (1)

cubfits-guide PDF

How these are measured

Downloads

8.4K

CRAN downloads in the past year

Rank #6,576 · ~23/day · ~701/mo

Releases R versions

Daily download trend is not available in this view yet.

46930 days

1.3K90 days

8.4K1 year

Compare downloads with other packages →

Also on394 r2u11 autocran179 c2d4u

How downloads are counted

Repository

snoweye/cubfits ↗Account: snoweye

7Stars

7Forks

0Open issues

0Open PRs

0Releases

174Commits

6Commit identities

License file reads as MPL-2.0 · 174 commits · Last activity 2021-11-07

Responsiveness

How these are sampled

PRs merged (all time): 92%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2024-06-24 · 72026-07-07 · 7

How these are measured

PracticesBeta

Checks run against github.com/snoweye/cubfits on 2026-10-11.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing cubfits adds 3 packages (0 with compiled code, 454 KB of source tarballs). Heaviest: iterators 293 KB, foreach 88 KB, coda 73 KB.

Depends (8)

R >= 4.0.0methodscoda foreachparallelstatsgraphicsutils

Imports (0)

none

LinkingTo (0)

none

Suggests (3)

seqinr VGAM EMCluster

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 (8)

Wei-Chen Chen

Author, Maintainer since 0.1-0 (2014)

Michael A. Gilchrist

Author · added in 0.1-2

William Howell

Author

Cedric Landerer

Author · added in 0.1-2

Drew Schmidt

Author

Russell Zaretzki

Author

Preston Hewgley

Contributor · added in 0.1-2

Students REU13

Contributor

Listed in earlier versions (1)

Michael Gilchrist

no longer listed · 0.1-0

Releases (4)

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
unarchivedReturned to CRAN
2021-11-07
0.1-4Latest
record
2021-11-07 · current release · diff ↗
archivedRemoved from CRAN
2021-11-05
check problems were not corrected in time
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
R
R 3.5.0 released · 2018-04-23
0.1-3
record
2017-04-30 · diff ↗
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
0.1-2
record
2016-01-24 · diff ↗ ·
added 12 exports
plotCUB.NSE, prop.model.nse, plotbin.NSE, plotCUB, plotTraces, plotBMatrixPosterior, plotExpectedPhiTrace, plotPTraces, readGenome, cubmultichain, cubsinglechain, normalizeDataSet

Show 3 earlier eventsHide 3 earlier events

R
R 3.2.0 released · 2015-04-16
0.1-0
record
2014-05-19
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2014-05-19
Total releases: 4 / 12 yrs
License: Mozilla Public License 2.0
Minimum R: ≥ 4.0.0
Bundled data: 221 KB / 10 files
Download size: 1.1 MB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("cubfits")

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

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 cubfits version 0.1-4 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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