Diagnostics for Soil-Plant-Microbial Redox Recovery
Overview
Provides diagnostic functions for integrating longitudinal soil, plant and microbial observations during redox disturbance and recovery. Functions calculate stoichiometric potential oxygen demand, accessible electron capacity from explicitly supplied inventories and kinetic parameters, recovery signatures, fixed-reference domain scores, and exploratory multiblock scores with observation-coverage diagnostics. Memory is represented as a holobiont state accumulating from mineralogical, plant-acclimation and microbial-community legacies. An illustrative simulator produces closed Fe and Mn inventories alongside synthetic observations; its carbon, nitrogen, sulfur and oxygen budgets are not closed and its parameters are not calibrated to field rates. Simulation benchmarks assess agreement with a prescribed synthetic target and do not constitute empirical validation or parameter identification. Accuracy assessment is cluster-aware: intervals come from resampling whole trajectories, agreement is reported as Lin's concordance coefficient alongside correlation, and mean squared error is partitioned into bias, variance mismatch and lack of correlation. The measured quantities follow Sander, Hofstetter and Gorski (2015) doi:10.1021/acs.est.5b00006 for mediated electrochemical determination of electron-accepting and electron-donating capacity, Kluepfel, Piepenbrock, Kappler and Sander (2014) doi:10.1038/ngeo2084 for regeneration of electron-accepting capacity across repeated anoxic periods, Thompson, Chadwick, Rancourt and Chorover (2006) doi:10.1016/j.gca.2005.12.005 for the increase in iron-oxide crystallinity under redox oscillation, and Keiluweit, Wanzek, Kleber, Nico and Fendorf (2017) doi:10.1038/s41467-017-01406-6 for anaerobic microsites in otherwise aerobic soil. Agreement statistics follow Lin (1989) doi:10.2307/2532051 and Kobayashi and Salam (2000) doi:10.2134/agronj2000.922345x.
- Resubmission of 1.0.8 with <what changed>.
From NEWS.md in the release
Install
Health
- OK13 OKNow
- OK3 OK2026-09-23
Documentation
- Help pages
- 40 (1 internal)includes a package overview page
- Examples that run
- 62%24 run in a plain check · 15 only when donttest examples are enabled (R CMD check --as-cran)
- Exported functions with examples
- 100%
- Documented parameters
- 80%
- Return-value docs
- 100%
- Help pages citing references
- 5%
Downloads
Repository
Commits over time
5 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/mghotbi/hrri on 2026-10-18.
The R CMD check workflow runs on macOS
GitHub Pages site last deployed 2026-10-04 · The repository has a site deploy workflow
pkgdown site last built 2026-10-04, before release 1.0.9 (2026-10-05)
Dependencies
Installing HRRI adds 30 packages (16 with compiled code, 33 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, igraph 4.8 MB.
Code & Tests
People & History
Pick two releases to compare their code metrics.
- 1.0.9Latest2026-10-05 · current release · diff ↗ ··
added 3 exports
plot_rri_framework, plot_rri_identifiability, plot_rri_recovery_diagnostics8 hours in CRAN's queue
Listed in CRAN's incoming queue from 2026-10-04 12:59 to 2026-10-04 20:43 UTC, in 3 readings. - 1.0.62026-09-23
- RR 4.6.0 released · 2026-04-24
Package metadata
- First published
- 2026-09-23
- Total releases
- 2 / 1 yrs
- License
- MIT + file LICENSE OSI
- Minimum R
- ≥ 4.3.0
- Download size
- 3.9 MB
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("HRRI")The package provides a citation file that builds its entry when R runs it. Run citation() to see it.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
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.