Package index • HRRI

Simulation and bundled example inputs

Generate illustrative soil–plant–microbe trajectories and the declared reservoir template used by the demonstrations.

simulate_redox_holobiont(): Simulate illustrative soil-plant-microbe redox trajectories
rri_simulation_demo(): Reproducible observable-only HRRI demonstration
rri_default_reservoirs(): Illustrative reservoir parameter template
HRRI_workflow_example redoxrri_example: Worked example: a complete HRRI workflow

Quantities computed from inventories, accessibility and exchange rates that the user supplies. These are never estimated from the scores.

rri_accessible_capacity(): Event-window accessible reservoir capacities
rri_o2_demand(): Stoichiometric O\(_2\) Demand from Reduced-Pool Inventories

Build oriented soil, plant and microbial scores, with coverage and missingness retained rather than recoded as zero.

rri_pipeline(): Score observed soil, plant and microbial panels
rri_pipeline_st(): Exploratory domain-score integration (legacy interface)
attach_hrri_ids(): Attach design identifiers to a score table with explicit alignment checks
rri_reference_scores(): Score departures from an explicitly defined reference
rri_capacity_index(): Oxidative-oriented soil feature composite
rri_root_physio(): Exploratory root-trait composite
rri_micro_functional_score(): Construct an explicitly weighted microbial guild contrast
rri_kinetics_score(): Descriptive recovery speed score
rri_connectivity_score(): Cross-domain association or graph-topology summary
rri_compensation_index(): Cross-domain asynchrony diagnostic

Descriptive diagnostics for a single disturbance, reported with fit status and estimability so an unsupported quantity stays missing.

rri_recovery_metrics(): Descriptive recovery metrics for a single disturbance
rri_memory_index(): Persistent-displacement and loop-area diagnostic

Compare a score with a reference target while respecting clustering, and probe how the result depends on weights and specification.

rri_accuracy() print(<rri_accuracy>): Agreement between a score and a reference target, respecting clustering
rri_latent_correlation(): Correlation with a Simulator-Defined Target
rri_property_scores(): Summarise supported diagnostics without fabricating missing properties
rri_domain_influence(): Realised influence of each domain on the composite score
rri_sensitivity(): Sensitivity to domain aggregation weights
benchmark_hrri() print(<hrri_benchmark>): Benchmark diagnostic agreement with a simulator-defined target
hrri_infer_architecture() print(<hrri_arch>) summary(<hrri_arch>) as.data.frame(<hrri_arch>) validate_architecture() print(<hrri_arch_validation>): Fit a conditional capacity-recovery curve (legacy function name)

Publication figures used in the manuscript, plus the general-purpose diagnostic plots and the shared theme.

plot_rri_framework(): Complementary mechanistic and observational routes
plot_rri_identifiability(): Identifiability, sensitivity and oxygen-accounting illustrations
plot_rri_timeseries(): Aligned time series with separate physical units
plot_rri_recovery_diagnostics(): Aligned score trajectories and recovery-descriptor availability
plot_rri_properties(): Profile of Available HRRI Diagnostics
plot_rri_accuracy(): Four-panel diagnostic figure for an accuracy assessment
plot_rri_recovery_map(): Plot RRI Recovery Map
plot_rri_recovery_landscape(): Plot a recovery landscape from RRI perturbation-recovery metrics
plot_rri_state_space(): Plot domain-score space with correctly matched trajectory diagnostics
plot_rri_validation(): Scatter of HRRI score against a simulator-defined target
plot_RRI_ternary(): Ternary Plot of Relative Domain Scores
plot_hrri_benchmark(): Plot descriptive benchmark agreement
plot_rri_simulation_demo(): Draw the reproducible simulation demonstration
theme_ems(): EMS plotting theme