R Observatory: Metrics for pam version 2.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pam

2.3.0

Fast and Efficient Processing of PAM Data

0packages depend

7.2Kdownloads / year

90.0%test coverage

13/13checks pass

Overview

About

Maintained by Julien BöhmFirst published 2025-01-1412 releasesCRAN page ↗GitHub ↗

Processing Chlorophyll Fluorescence & P700 Absorbance data. Four models are provided for the regression of Pi curves, which can be compared with each other in order to select the most suitable model for the data set. Control plots ensure the successful verification of each regression. Bundled output of alpha, ETRmax, Ik etc. enables fast and reliable further processing of the data.

Install

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

install.packages("pam", 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("biotoolbox/pam")

Development version from biotoolbox/pam. 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-pam

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

# 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-pam

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-pam

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 2.8 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 1.18

90.0%

Coverage · measured lines

100%

Documentation · exports

8

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 65%
References docs: 46%

Downloads

7.2K

CRAN downloads in the past year

Rank #7,196 · ~20/day · ~602/mo

Releases R versions

Daily download trend is not available in this view yet.

22130 days

1.2K90 days

7.2K1 year

Compare downloads with other packages →

Also on154 r2u14 autocran

Repository

GitHub ↗ biotoolbox/pam

6Stars

2Forks

0Open issues

0Open PRs

13Releases

234Commits

2Contributors

pamphotosynthesisbiological-data-analysislight-curvelight-curve-modelsrapid-light-curve

License GPL-3.0 · 234 commits · Last activity 2026-07-09 · 0% stars, 30d

Stars over time

2025-01-20 · 32026-07-07 · 6

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/biotoolbox/pam on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

Makefile

Research and citation (1)

CITATION.cff

Lint, format, editor (1)

EditorConfig

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

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (8)

rlang data.table ggplot2 minpack.lm cowplot gridExtra ggthemes Metrics

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Julien Böhm

Maintainer, Author

Authors (2)

Julien Böhm

Maintainer, Author

Philipp Schrag

Author

Package Timeline

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

2.3.0Latest
2026-07-08 · current release · diff ↗
2.2.1
2026-04-30 · diff ↗
R
R 4.6.0 released · 2026-04-24
2.2.0
2026-04-23 · diff ↗
2.1.1
2026-04-11 · diff ↗
2.1.0
2026-04-11 · diff ↗
2.0.2
2026-02-23 · diff ↗
2.0.0
2026-02-01 · diff ↗
1.0.6
2025-08-27 · diff ↗
1.0.4
2025-07-29 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.2
2025-02-25 · diff ↗
1.0.1
2025-01-15 · diff ↗
1.0.0
2025-01-14
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-01-14
Total releases: 12 / 1 yrs
License: GPL-3 OSI
Download size: 74 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("pam")

The authors publish a CITATION.cff, so they have said how they want this cited. Run citation() and use what it gives you.

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 pam version 2.3.0 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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