R Observatory: Metrics for chem16S version 1.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

chem16S

1.2.0Package record

Chemical Metrics for Microbial Communities

0packages depend

2.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Jeffrey DickCRAN page ↗GitHub ↗

Combines taxonomic classifications of high-throughput 16S rRNA gene sequences with reference proteomes of archaeal and bacterial taxa to generate amino acid compositions of community reference proteomes. Calculates chemical metrics including carbon oxidation state ('Zc'), stoichiometric oxidation and hydration state ('nO2' and 'nH2O'), H/C, N/C, O/C, and S/C ratios, grand average of hydropathicity ('GRAVY'), isoelectric point ('pI'), protein length, and average molecular weight of amino acid residues. Uses precomputed reference proteomes for archaea and bacteria derived from the Genome Taxonomy Database ('GTDB'). Also includes reference proteomes derived from the NCBI Reference Sequence ('RefSeq') database and manual mapping from the 'RDP Classifier' training set to 'RefSeq' taxonomy as described by Dick and Tan (2023) doi:10.1007/s00248-022-01988-9. Processes taxonomic classifications in 'RDP Classifier' format or OTU tables in 'phyloseq-class' objects from the Bioconductor package 'phyloseq'.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("chem16S", 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("jedick/chem16S")

Development version from jedick/chem16S. 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-chem16s

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 4.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
NOTE12 OK, 1 NOTE2026-06-08
OK14 OK2026-03-16

Show 3 earlier changesHide 3 earlier changes

ERROR13 OK, 1 ERROR2026-03-13
OK14 OK2026-03-12
ERROR13 OK, 1 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.0

READMEYes · 392 wordsVignettesYes · 3 · dynamicNEWSYes · 33% structuredCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 10includes a package overview page
Examples that run: 100%9 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 50%

Vignettes (3)

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #13,006 · ~8/day · ~238/mo

Releases R versions

Daily download trend is not available in this view yet.

28530 days

88890 days

2.9K1 year

Compare downloads with other packages →

Also on171 r2u

How downloads are counted

Repository

jedick/chem16s ↗Account: jedick

4Stars

0Forks

0Open issues

0Open PRs

7Releases

117Commits

1Commit identities

16s-rrnachemical-metricsrcarbon-oxidation-stategenomic-adaptationmicrobial-communities

License file reads as GPL-3.0 · 117 commits · Last activity 2025-09-13 · Default branch at 1.2.0-6, ahead of CRAN 1.2.0 (checked 2026-10-25)

Responsiveness

not measured

Stars over time

2024-04-23 · 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/jedick/chem16s on 2026-10-25.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Coverage (1)

Coverage reporting

Research and citation (1)

CITATION.cff

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

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing chem16S adds 25 packages (12 with compiled code, 28 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, Rcpp 1.8 MB. 1 more not on CRAN is not measured.

Depends (1)

R >= 3.5.0

Imports (6)

plyr ggplot2 rlang reshape2 phyloseq canprot

LinkingTo (0)

none

Suggests (5)

tinytest knitr patchwork ggpmisc rmarkdown

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)

Jeffrey Dick

Author, Maintainer since 1.0.0 (2023)

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
1.2.0Latest
record
2025-01-16 · current release · diff ↗ ·
added 1 export
get_metric_byrank
1.1.0
record
2024-07-01 · diff ↗ ·
removed 2 exports
add_hull, calc_metrics
R
R 4.4.0 released · 2024-04-24
1.0.0
record
2023-07-17
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-07-17
Total releases: 3 / 3 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 48 KB / 3 files
Download size: 3.5 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("chem16S")

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

It points to 10.1093/bioinformatics/btad564.

The repository also keeps a CITATION.cff.

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 chem16S version 1.2.0 [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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