R Observatory: Metrics for phytoclass version 2.3.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phytoclass

2.3.1Package record

Estimate Chla Concentrations of Phytoplankton Groups

0packages depend

4.1Kdownloads / year

56.3%test coverage

13/13flavors OK

Overview

About

Maintained by Alexander HaywardCRAN page ↗GitHub ↗Issues ↗

Determine the chlorophyll a (Chl a) concentrations of different phytoplankton groups based on their pigment biomarkers. The method uses non-negative matrix factorisation and simulated annealing to minimise error between the observed and estimated values of pigment concentrations (Hayward et al. (2023) doi:10.1002/lom3.10541). The approach is similar to the widely used 'CHEMTAX' program (Mackey et al. 1996) doi:10.3354/meps144265, but is more straightforward, accurate, and not reliant on initial guesses for the pigment to Chl a ratios for phytoplankton groups.

Changes in 2.3.1

Enhancements

Updated min_max.rda using new pigment ratio min/max from Simon Wright.
Improve "custom-example" vignette to use southern ocean min_max.

From NEWS.md in the release

Install

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

install.packages("phytoclass", 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("phytoclass/phytoclass")

Development version from phytoclass/phytoclass. 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-phytoclass

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-phytoclass

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-phytoclass

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

13OK

CRAN check page ↗

Slowest check: 5.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-30

Show 2 earlier changesHide 2 earlier changes

ERROR13 OK, 1 ERROR2026-03-28
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.3.1

READMEYes · 273 wordsVignettesYes · 5 · dynamicNEWSYes · 67% structured · mentions 2.3.1Citation fileNo

Help pages: 33 (19 internal)
Examples that run: 92%22 run in a plain check · 2 hold no code
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (5)

How these are measured

Downloads

4.1K

CRAN downloads in the past year

Rank #15,068 · ~11/day · ~343/mo

Releases R versions

Daily download trend is not available in this view yet.

32730 days

79990 days

4.1K1 year

Compare downloads with other packages →

Also on82 r2u3 autocran

How downloads are counted

Repository

phytoclass/phytoclass ↗Organization: phytoclass

7Stars

5Forks

11Open issues

1Open PRs

0Releases

843Commits

8Commit identities

843 commits · Last activity 2026-04-10 · 0% stars, 30d · Default branch at 3.0.0, ahead of CRAN 2.3.1 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 93%
Median days to close, 50 most recently updated closed issues: 54
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-05-10 · 32026-07-28 · 7

How these are measured

PracticesBeta

10 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/phytoclass/phytoclass on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (1)

Contributing guide

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-04-10 · The repository has a site deploy workflow

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 1 practice

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

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

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing phytoclass adds 75 packages (35 with compiled code, 50 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 3.8

Imports (7)

bestNormalize dynamicTreeCut ggplot2 RcppMLstatstidyr progress

LinkingTo (0)

none

Suggests (5)

knitr rmarkdown testthat quarto here

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 (5)

Alexander Hayward

Sebastian Di Geronimo

Author · added in 2.3.1

Mohd Aasim Maqsood Khan

Author · added in 2.3.1

Andy McKenzie

Author

Tylar Murray

Author · added in 2.0.0

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
2.3.1Latest
record
2026-01-30 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
2.0.0
record
2024-11-14 · diff ↗
1.2.0
record
2024-05-11 · diff ↗ ·
added 1 export
simulated_annealing_Prochloro
R
R 4.4.0 released · 2024-04-24
1.0.0
record
2023-09-29
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-09-29
Total releases: 4 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.8
Bundled data: 6.1 KB / 5 files
Download size: 422 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("phytoclass")

Format

Hayward, A., Di Geronimo, S., Khan, M. A. M., McKenzie, A., & Murray, T. (2026). phytoclass: Estimate Chla Concentrations of Phytoplankton Groups (Version 2.3.1) [Computer software]. https://doi.org/10.32614/CRAN.package.phytoclass

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 phytoclass version 2.3.1 [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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