chem16S

1.2.0

Chemical Metrics for Microbial Communities

0packages depend

2.6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Jeffrey DickFirst published 2023-07-173 releasesCRAN 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.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

13OK

Slowest check: 5.9 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-06-08
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-16
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-13
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-12
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 1 earlier snapshots

ERROR2026-03-10
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Documentation

READMEYes · 392 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 45%

Downloads

2.6K

CRAN downloads in the past year

Rank #14,401 · ~7/day · ~214/mo

Releases R versions

Daily download trend is not available in this view yet.

25230 days

76790 days

2.6K1 year

Compare downloads with other packages →

Also on228 r2u

Repository

GitHub ↗ jedick/chem16s

4Stars

0Forks

0Open issues

0Open PRs

7Releases

117Commits

1Contributors

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

License GPL-3.0 · 117 commits · Last activity 2025-09-13

Stars over time

2024-04-23 · 42026-07-07 · 4

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/jedick/chem16s on 2026-07-19.

Continuous integration (1)

GitHub Actions

Research and citation (1)

CITATION.cff

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

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.

Code & Tests

Code Composition

Vignettes 887 (28%)Rd 857 (27%)R 848 (27%)Other 568 (18%)CSS 38 (1%)

Code characteristics

Cyclomatic complexity: 7.5 median / 20 max
Test cases: 35 / 0.00 per code line

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

12 11 exported

Complexity

9.1 avg / 20 max

Call network

12 nodes / 8 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (1)

Maintainer (1)

Jeffrey Dick

Author, Maintainer

Authors (1)

Jeffrey Dick

Author, Maintainer

Package Timeline

3 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.2.0Latest
2025-01-16 · current release · diff ↗
1.1.0
2024-07-01 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.0.0
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
Installed size: not tracked yet
With dependencies: not tracked yet

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