{ "_id": "6ac254dad743750d376d7fa0", "Package": "HRRI", "Type": "Package", "Title": "Diagnostics for Soil-Plant-Microbial Redox Recovery", "Version": "1.0.9", "Date": "2026-10-04", "Authors@R": "c(\nperson(\"Mitra\", \"Ghotbi\",\nemail = \"mitra.ghotbi@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-9185-9993\")),\nperson(\"Marjan\", \"Ghotbi\",\nemail = \"ghotbi.marjan@gmail.com\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0003-4655-6445\")))", "Description": "Provides diagnostic functions for integrating longitudinal\nsoil, plant and microbial observations during redox disturbance\nand recovery. Functions calculate stoichiometric potential\noxygen demand, accessible electron capacity from explicitly\nsupplied inventories and kinetic parameters, recovery\nsignatures, fixed-reference domain scores, and exploratory\nmultiblock scores with observation-coverage diagnostics. Memory\nis represented as a holobiont state accumulating from\nmineralogical, plant-acclimation and microbial-community\nlegacies. An illustrative simulator produces closed Fe and Mn\ninventories alongside synthetic observations; its carbon,\nnitrogen, sulfur and oxygen budgets are not closed and its\nparameters are not calibrated to field rates. Simulation\nbenchmarks assess agreement with a prescribed synthetic target\nand do not constitute empirical validation or parameter\nidentification. Accuracy assessment is cluster-aware: intervals\ncome from resampling whole trajectories, agreement is reported\nas Lin's concordance coefficient alongside correlation, and\nmean squared error is partitioned into bias, variance mismatch\nand lack of correlation. The measured quantities follow Sander,\nHofstetter and Gorski (2015) for\nmediated electrochemical determination of electron-accepting\nand electron-donating capacity, Kluepfel, Piepenbrock, Kappler\nand Sander (2014) for regeneration of\nelectron-accepting capacity across repeated anoxic periods,\nThompson, Chadwick, Rancourt and Chorover (2006)\n for the increase in iron-oxide\ncrystallinity under redox oscillation, and Keiluweit, Wanzek,\nKleber, Nico and Fendorf (2017)\n for anaerobic microsites in\notherwise aerobic soil. Agreement statistics follow Lin (1989)\n and Kobayashi and Salam (2000)\n.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "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": { "Date": "2026-10-04 13:24:40 UTC", "User": "root" }, "Author": "Mitra Ghotbi [aut, cre]\n(), Marjan Ghotbi [ctb]\n()", "Maintainer": "Mitra Ghotbi ", "Config/pak/sysreqs": "libglpk-dev libicu-dev libxml2-dev", "Repository": "https://mghotbi.r-universe.dev", "Date/Publication": "2026-10-04 09:59:07 UTC", "RemoteUrl": "https://github.com/mghotbi/hrri", "RemoteRef": "HEAD", "RemoteSha": "cce9e1ea927d42dea4798133aa1acdf848e29340", "_user": "mghotbi", "_type": "src", "_file": "HRRI_1.0.9.tar.gz", "_fileid": 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