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
Config/testthat/edition: 3
Config/roxygen2/version: 8.1.0
NeedsCompilation: no
Packaged: 2026-09-13 14:45:59 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>
Repository: CRAN
Date/Publication: 2026-09-23 04:30:02 UTC
