R Observatory: Metrics for EBASE version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

EBASE

1.1.0Package record

Estuarine Bayesian Single-Station Estimation Method for Ecosystem Metabolism

0packages depend

2.8Kdownloads / year

97.5%test coverage

0/13flavors OK

Overview

About

Maintained by Marcus BeckCRAN page ↗GitHub ↗Website ↗Issues ↗

Estimate ecosystem metabolism in a Bayesian framework for individual water quality monitoring stations with continuous dissolved oxygen time series. A mass balance equation is used that provides estimates of parameters for gross primary production, respiration, and gas exchange. Methods adapted from Grace et al. (2015) doi:10.1002/lom3.10011 and Wanninkhof (2014) doi:10.4319/lom.2014.12.351. Details in Beck et al. (2024) doi:10.1002/lom3.10620.

Changes in 1.1.0

Added nogas argument option to ebase() to estimate EBASE without gas exchange
Removed option for progress file output from ebase() which can unexpectedly cause JAGS to crash
Added ebase_years() function to estimate EBASE on multiple years of data
Added net ecosystem metabolism (NEM) as output from ebase()
Added asnem argument as option to plot NEM, P, and R using ebase_plot()

From NEWS.md in the release

Install

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

install.packages("EBASE", 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("fawda123/EBASE")

Development version from fawda123/EBASE. 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-ebase

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-EBASE

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-EBASE

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

13NOTE

Check messages

NOTEDESCRIPTION meta-informationr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘ebase_plot.R’ ‘ebase_prep.R’

r-devel-windows-x86_64, r-oldrel-windows-x86_64, r-release-windows-x86_64

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'ebase_plot.R' 'ebase_prep.R'

CRAN check page ↗

Slowest check: 6.6 min · r-oldrel-windows-x86_64

Status changes

NOTE13 NOTE2026-09-26
ERROR12 NOTE, 1 ERROR2026-09-25
NOTE13 NOTE2026-07-31
ERROR12 NOTE, 1 ERROR2026-07-30
NOTE13 NOTE2026-06-29

Show 4 earlier changesHide 4 earlier changes

ERROR12 NOTE, 1 ERROR2026-06-27
NOTE13 NOTE2026-06-01
ERROR12 NOTE, 1 ERROR2026-05-30
NOTE3 OK, 11 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.0

READMEYes · 60 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.1.0Citation fileNoWebsiteYes · pkgdown

Help pages: 16
Examples that run: 100%15 run in a plain check
Exported functions with examples: 93%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 19%

Vignettes (1)

EBASE overview HTML

How these are measured

Downloads

2.8K

CRAN downloads in the past year

Rank #15,575 · ~8/day · ~229/mo

Releases R versions

Daily download trend is not available in this view yet.

30830 days

79490 days

2.8K1 year

Compare downloads with other packages →

Also on73 r2u5 autocran

How downloads are counted

Repository

fawda123/ebase ↗Account: fawda123

0Stars

0Forks

0Open issues

0Open PRs

4Releases

221Commits

1Commit identities

metabolism

License file reads as CC0-1.0 · 221 commits · Last activity 2024-09-25

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 2
Median days to close, 50 most recently updated closed PRs: not measured

Releases over time

2024-09-25 · 42026-07-07 · 4

How these are measured

PracticesBeta

12 development-tooling and community-health practices detected across 7 families in the upstream repository

Checks run against github.com/fawda123/ebase on 2026-10-21.

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 (3)

Code of conductContributing guideIssue templates

Docs source (3)

pkgdown

GitHub Pages site last deployed 2024-09-25 · The repository has a site deploy workflow

pkgdown site last built 2024-09-25

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 3 practices

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing EBASE adds 41 packages (20 with compiled code, 31 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, isoband 1.5 MB.

Depends (1)

R >= 3.5

Imports (10)

doParallel dplyr foreach ggplot2 lubridate R2jags rjags tidyr truncnorm zoo

LinkingTo (0)

none

Suggests (4)

testthat knitr rmarkdown covr

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 (4)

Marcus Beck

Author, Maintainer since 1.0.0 (2024)

Jill Arriola

Author

Maria Herrmann

Author

Raymond Najjar

Author

Releases (4)

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
1.1.0Latest
record
2024-09-25 · current release · diff ↗ ·
added 1 export
ebase_years
1.0.2
record
2024-06-04 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.0.1
record
2024-03-22 · diff ↗
1.0.0
record
2024-03-08
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-03-08
Total releases: 4 / 2 yrs
License: CC0
Minimum R: ≥ 3.5
Bundled data: 213 KB / 2 files
Download size: 847 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("EBASE")

Format

Beck, M., Arriola, J., Herrmann, M., & Najjar, R. (2024). EBASE: Estuarine Bayesian Single-Station Estimation Method for Ecosystem Metabolism (Version 1.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.EBASE

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 EBASE version 1.1.0 [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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