R Observatory: Metrics for pam version 2.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pam

2.3.0Package record

Fast and Efficient Processing of PAM Data

0packages depend

7Kdownloads / year

90.0%test coverage

13/13flavors OK

Overview

About

Maintained by Julien BöhmCRAN page ↗GitHub ↗Issues ↗

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. 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-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). 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: 2.6 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 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.3.0

READMENoVignettesNoNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 37
Examples that run: 100%24 run in a plain check
Exported functions with examples: 65%
Documented parameters: 100%
Return-value docs: 65%
Help pages citing references: 46%

How these are measured

Downloads

7K

CRAN downloads in the past year

Rank #6,874 · ~19/day · ~583/mo

Releases R versions

Daily download trend is not available in this view yet.

48230 days

1.3K90 days

7K1 year

Compare downloads with other packages →

Also on122 r2u3 autocran

How downloads are counted

Repository

biotoolbox/pam ↗Organization: biotoolbox

6Stars

2Forks

0Open issues

0Open PRs

13Releases

234Commits

2Commit identities

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

License file reads as GPL-3.0 · 234 commits · Last activity 2026-07-08 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 80%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-01-20 · 32026-07-07 · 6

How these are measured

PracticesBeta

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

Checks run against github.com/biotoolbox/pam on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Reproducibility and dev environment (1)

Makefile

Research and citation (1)

CITATION.cff

Lint, format, editor (1)

EditorConfig

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

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing pam adds 29 packages (13 with compiled code, 25 MB of source tarballs). Heaviest: ggplot2 6.0 MB, data.table 5.7 MB, ggthemes 2.1 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Julien Böhm

Maintainer since 1.0.0 (2025), Author

Philipp Schrag

Author

Releases (12)

Pick two releases to compare their code metrics.

2.3.0Latest
record
2026-07-08 · current release · diff ↗ ·
added 1 export
read_diving_pam_II_data
2.2.1
record
2026-04-30 · diff ↗
R
R 4.6.0 released · 2026-04-24
2.2.0
record
2026-04-23 · diff ↗ ·
added 3 exports
read_dual_pam_single_channel_fluo_data, read_dual_pam_single_channel_p700_data, read_pam_2500_data
2.1.1
record
2026-04-11 · diff ↗
2.1.0
record
2026-04-11 · diff ↗
2.0.2
record
2026-02-23 · diff ↗
2.0.0
record
2026-02-01 · diff ↗ ·
added 1 export
read_universal_data
1.0.6
record
2025-08-27 · diff ↗
1.0.4
record
2025-07-29 · diff ↗ ·
added 1 export
read_junior_pam_data
R
R 4.5.0 released · 2025-04-11
1.0.2
record
2025-02-25 · diff ↗
1.0.1
record
2025-01-15 · diff ↗
1.0.0
record
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

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("pam")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 pam version 2.3.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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