R Observatory: Metrics for SIPmg version 3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2025-10-10. Its history is shown below.

Reason: check issues were not corrected in time

Details below reflect version 3.0, its last release before removal.

SIPmg

3.0Package record

Statistical Analysis to Identify Isotope Incorporating Metagenomic Features

0packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Pranav SamparaCRAN page ↗Website ↗

Statistical analysis as part of a quantitative stable isotope probing (SIP) metagenomics study to identify isotope incorporating metagenomic features. Helpful reading and a vignette in bookdown format is provided on the package site https://zielslab.github.io/SIPmg.github.io/.

Install

R (source archive)

url <- "https://cran.r-project.org/src/contrib/Archive/SIPmg/SIPmg_3.0.tar.gz"
pkgFile <- "SIPmg_3.0.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 (3.0) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

Health

CRAN checks

CRAN check results are not tracked yet.

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.0

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsiteYes

Help pages: 31
Examples that run: 100%12 run in a plain check
Exported functions with examples: 80%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

SIPmg Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on308 r2u

How downloads are counted

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (17)

data.table DESeq2 dplyr ggplot2 ggpubr glue lazyeval magrittrMASSphyloseq plyr purrr rlang stringr tibble tidyrutils

LinkingTo (0)

none

Suggests (6)

BiocManager EBImage knitr readr rmarkdown tidyverse

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 (4)

Pranav Sampara

Author, Maintainer since 1.4 (2023)

Ryan Ziels

Author

Alma Garcia Roche

Author · added in 3.0

Kate Waring

Contributor

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
archivedRemoved from CRAN
2025-10-10
check issues were not corrected in time
unarchivedReturned to CRAN
2025-09-24
3.0
record
2025-09-24 · diff ↗ ·
added 3 exports
as.Num, phyloseq2df, phyloseq2table
R
R 4.5.0 released · 2025-04-11
archivedRemoved from CRAN
2024-11-18
requires archived package 'HTSSIP'
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.4.1
record
2023-02-21 · diff ↗
1.4
record
2023-01-16
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-01-16
Total releases: 3 / 3 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.5.0
Bundled data: 183 KB / 12 files

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SIPmg")

Format

Sampara, P., Waring, K., Ziels, R., & Garcia Roche, A. (n.d.). SIPmg: Statistical Analysis to Identify Isotope Incorporating Metagenomic Features (Version 3.0) [Computer software]. Retrieved October 27, 2026, from https://CRAN.R-project.org/package=SIPmg

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 SIPmg version 3.0 [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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