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Package: HRRI
Type: Package
Title: Diagnostics for Soil-Plant-Microbial Redox Recovery
Version: 1.0.6
Date: 2026-09-12
Authors@R: c(
person("Mitra", "Ghotbi",
email = "mitra.ghotbi@gmail.com",
role = c("aut", "cre"),
comment = c(ORCID = "0000-0001-9185-9993")),
person("Marjan", "Ghotbi",
email = "ghotbi.marjan@gmail.com",
role = "ctb",
comment = c(ORCID = "0000-0003-4655-6445")))
Description: 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>.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.3.0)
Imports: ggplot2 (>= 3.4.0), graphics, grid, igraph (>= 1.5.0), rlang
(>= 1.1.0), stats, utils, tidyr, tidyselect
Suggests: ggtern (>= 3.4.0), knitr, patchwork (>= 1.2.0), psych,
rmarkdown, testthat (>= 3.0.0), viridis
VignetteBuilder: knitr
URL: https://github.com/mghotbi/HRRI, https://mghotbi.github.io/HRRI/
BugReports: https://github.com/mghotbi/HRRI/issues
Roxygen: list(markdown = TRUE)
Config/testthat/edition: 3
Config/roxygen2/version: 8.1.0
NeedsCompilation: no
Packaged: 2026-09-12 00:00:00 UTC; mitraghotbi
Author: Mitra Ghotbi [aut, cre] (ORCID:
<https://orcid.org/0000-0001-9185-9993>),
Marjan Ghotbi [ctb] (ORCID: <https://orcid.org/0000-0003-4655-6445>)
Maintainer: Mitra Ghotbi <mitra.ghotbi@gmail.com>