https://mghotbi.r-universe.devRecent package updates in mghotbiR-universehttps://github.com/mghotbi.pnghttps://mghotbi.r-universe.devSun, 04 Oct 2026 09:59:07 GMTmitra.ghotbi@gmail.com (Mitra Ghotbi)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>.https://github.com/r-universe/mghotbi/actions/runs/37205315299Sun, 04 Oct 2026 09:59:07 GMTHRRI1.0.9successhttps://mghotbi.r-universe.devhttps://github.com/mghotbi/hrriHRRI_workflow.RmdHRRI_workflow.htmlHRRI: Holobiont Redox Resilience Index — End-to-End Workflow2026-09-01 09:05:202026-10-04 08:59:10HRRI_gallery.RmdHRRI_gallery.htmlHRRI: Reading the Figures — A Worked Example2026-09-02 06:42:362026-10-04 09:54:36HRRI_paper_figures.RmdHRRI_paper_figures.htmlHRRI: Reproduce All Six Paper Figures in R2026-10-03 21:07:002026-10-04 08:59:10mitra.ghotbi@gmail.com (Mitra Ghotbi)Provides a reproducible and modular workflow for absolute microbial quantification using spike-in controls. Supports both single spike-in taxa and synthetic microbial communities with user-defined spike-in volumes and genome copy numbers. Compatible with 'phyloseq' and 'TreeSummarizedExperiment' (TSE) data structures. The package implements methods for spike-in validation, preprocessing, scaling factor estimation, absolute abundance conversion, bias correction, and normalization. Facilitates downstream statistical analyses with 'DESeq2', 'edgeR', and other Bioconductor-compatible methods. Visualization tools are provided via 'ggplot2', 'ggtree', and related packages. Includes detailed vignettes, case studies, and function-level documentation to guide users through experimental design, quantification, and interpretation.https://github.com/r-universe/bioc/actions/runs/36355141680Sun, 27 Sep 2026 19:39:25 GMTDspikeIn1.3.2successhttps://bioc.r-universe.devhttps://github.com/bioc/DspikeInDspikeIn-with-TSE.RmdDspikeIn-with-TSE.htmlDspikeIn with TSE2025-06-18 15:46:472026-09-27 19:39:25