R Observatory: Metrics for AnaCoDa version 0.1.4.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2026-02-02. Its history is shown below.

Reason: issues were not corrected in time

Details below reflect version 0.1.4.4, its last release before removal.

AnaCoDa

0.1.4.4Package record

Analysis of Codon Data under Stationarity using a Bayesian Framework

0packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Cedric LandererCRAN page ↗GitHub ↗

Is a collection of models to analyze genome scale codon data using a Bayesian framework. Provides visualization routines and checkpointing for model fittings. Currently published models to analyze gene data for selection on codon usage based on Ribosome Overhead Cost (ROC) are: ROC (Gilchrist et al. (2015) doi:10.1093/gbe/evv087), and ROC with phi (Wallace & Drummond (2013) doi:10.1093/molbev/mst051). In addition 'AnaCoDa' contains three currently unpublished models. The FONSE (First order approximation On NonSense Error) model analyzes gene data for selection on codon usage against of nonsense error rates. The PA (PAusing time) and PANSE (PAusing time + NonSense Error) models use ribosome footprinting data to analyze estimate ribosome pausing times with and without nonsense error rate from ribosome footprinting data.

Install

R (source archive)pak (dev)

url <- "https://cran.r-project.org/src/contrib/Archive/AnaCoDa/AnaCoDa_0.1.4.4.tar.gz"
pkgFile <- "AnaCoDa_0.1.4.4.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (0.1.4.4) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

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

Development version from clandere/AnaCoDa. Installs pak first if it is not already available.

Health

CRAN checks

CRAN check results are not tracked yet.

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.4.4

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 83
Examples that run: 87%26 run in a plain check · 4 never run
Exported functions with examples: 83%
Documented parameters: 100%
Return-value docs: 94%
Help pages citing references: 0%

How these are measured

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on363 r2u26 autocran82 c2d4u

How downloads are counted

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (5)

R >= 3.3.0Rcpp VGAMmethodsmvtnorm

Imports (0)

none

LinkingTo (1)

Rcpp

Suggests (6)

knitr Hmisc coda testthat lmodel2 markdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Authors@R

Contributor · added in 0.1.4.4

Maintainer since 0.1.0 (2018)

Listed in earlier versions (5)

Show 5 peopleHide 5 people

Alex Cope

no longer listed · 0.1.0 to 0.1.3.0

Gabriel Hanas

no longer listed · 0.1.0 to 0.1.3.0

Cedric Landerer

no longer listed · 0.1.0 to 0.1.3.0

Jeremy Rogers

no longer listed · 0.1.0 to 0.1.3.0

Denizhan Pak

no longer listed · 0.1.2 to 0.1.3.0

Releases (8)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
archivedRemoved from CRAN
2026-02-02
issues were not corrected in time
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
0.1.4.4
record
2020-09-15 · diff ↗ ·
added 1 export
calculateMarginalLogLikelihood
R
R 4.0.0 released · 2020-04-24
unarchivedReturned to CRAN
2019-05-12
0.1.3.0
record
2019-05-11 · diff ↗
R
R 3.6.0 released · 2019-04-26
archivedRemoved from CRAN
2019-03-19
memory-access errors were not corrected despite updates
0.1.2.3
record
2019-03-15 · diff ↗
0.1.2.2
record
2019-03-04 · diff ↗
0.1.2.1
record
2018-11-27 · diff ↗

Show 5 earlier eventsHide 5 earlier events

0.1.2
record
2018-09-14 · diff ↗ ·
added 4 exports
findOptimalCodon, geomMean, getCodonCounts, calculateSCUO
R
R 3.5.0 released · 2018-04-23
0.1.1
record
2018-02-12 · diff ↗ ·
added 5 exports
getSelectionCoefficients, getCAIweights, getCAI, getNc, getNcAA
0.1.0
record
2018-01-11
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2018-01-11
Total releases: 8 / 8 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.3.0

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("AnaCoDa")

Format

Authors@R, . (n.d.). AnaCoDa: Analysis of Codon Data under Stationarity using a Bayesian Framework (Version 0.1.4.4) [Computer software]. Retrieved October 22, 2026, from https://CRAN.R-project.org/package=AnaCoDa

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 AnaCoDa version 0.1.4.4 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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