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# CITATION.cff file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "HRRI" in publications use:'
type: software
license: MIT
title: 'HRRI: Diagnostics for Soil-Plant-Microbial Redox Recovery'
version: 1.0.9
identifiers:
- type: doi
  value: 10.32614/CRAN.package.HRRI
abstract: '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) <https://doi.org/10.1021/acs.est.5b00006>
  for mediated electrochemical determination of electron-accepting and electron-donating
  capacity, Kluepfel, Piepenbrock, Kappler and Sander (2014) <https://doi.org/10.1038/ngeo2084>
  for regeneration of electron-accepting capacity across repeated anoxic periods,
  Thompson, Chadwick, Rancourt and Chorover (2006) <https://doi.org/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) <https://doi.org/10.1038/s41467-017-01406-6>
  for anaerobic microsites in otherwise aerobic soil. Agreement statistics follow
  Lin (1989) <https://doi.org/10.2307/2532051> and Kobayashi and Salam (2000) <https://doi.org/10.2134/agronj2000.922345x>.'
authors:
- family-names: Ghotbi
  given-names: Mitra
  email: mitra.ghotbi@gmail.com
  orcid: https://orcid.org/0000-0001-9185-9993
preferred-citation:
  type: manual
  title: 'HRRI: Holobiont Redox Resilience Index for Integrative Stress Biology'
  authors:
  - family-names: Ghotbi
    given-names: Mitra
    email: mitra.ghotbi@gmail.com
    orcid: https://orcid.org/0000-0001-9185-9993
  - family-names: Ghotbi
    given-names: Marjan
    orcid: https://orcid.org/0000-0003-4655-6445
  year: '2026'
  notes: R package version 1.0.9
  url: https://github.com/mghotbi/HRRI
repository: https://mghotbi.r-universe.dev
repository-code: https://github.com/mghotbi/HRRI
commit: cce9e1ea927d42dea4798133aa1acdf848e29340
url: https://mghotbi.github.io/HRRI/
date-released: '2026-10-04'
contact:
- family-names: Ghotbi
  given-names: Mitra
  email: mitra.ghotbi@gmail.com
  orcid: https://orcid.org/0000-0001-9185-9993
references:
- type: unpublished
  title: 'HRRI: direction-aware diagnostics for soil-plant-microbiome redox recovery
    across hydroclimatic disturbances'
  authors:
  - family-names: Ghotbi
    given-names: Mitra
  - family-names: Ghotbi
    given-names: Marjan
  - family-names: Komluski
    given-names: Jovan
  - family-names: Holtgrewe-Stukenbrock
    given-names: Eva H.
  year: '2026'
  notes: Manuscript in preparation
- type: unpublished
  title: A Theory of Hydroclimatic Redox Resilience
  authors:
  - family-names: Ghotbi
    given-names: Mitra
  - family-names: Kolody
    given-names: Bethany C.
  - family-names: Ghotbi
    given-names: Marjan
  - family-names: Holtgrewe-Stukenbrock
    given-names: Eva
  year: '2026'
  notes: Submitted to Communications Earth & Environment
- type: unpublished
  title: 'Rhizosphere redox recovery after hydrological disturbances: mechanisms across
    the soil-plant-microbiome continuum'
  authors:
  - family-names: Ghotbi
    given-names: Mitra
  - family-names: Ghotbi
    given-names: Marjan
  - family-names: Muehling
    given-names: Karl H.
  - family-names: Stukenbrock
    given-names: Eva H.
  year: '2026'
  notes: Submitted to Soil Biology & Biochemistry