How to use this vignette | The experiment | The four hidden states, made visible | Memory is a holobiont state | Scoring the three domains | One trajectory in context | Where the domains sit relative to each other | Domain-score state space | Recovery signatures | Recovery map across all trajectories | Ranking trajectories by signature | Property diagnostics | Did HRRI recover the hidden state? | Using your own data | Complete paper figure set | Session information

Introduction | In-silico Data Generation | Design identifiers | Soil geochemical outputs | Fe mass-balance verification | Plant physiology | Microbial functional genes | Accessible-Capacity Estimation | Effect of event timescale τ | RRI Pipeline | Agreement with the prescribed target | Recovery Signatures | Disturbance-History Sensitivity | Publication figures | Session Information | References | Published methods | Companion manuscripts

One figure-to-function map | Figure 1: complementary routes | Figure 2: identifiability, sensitivity and accounting | Figure 3: forcing and responses | Figure 4: recovery diagnostics | Figure 5: operational properties | Figure 6: conditional agreement | Export without loss of quality | References | Published methods | Companion manuscripts

Acknowledgments | DspikeIn | DspikeIn requirements | To build TreeSummarizedExperiment file please refer to | spike-in validation | Did spike-ins behave as expected across all samples? | Pre_processing | Spiked species and related parameters should be defined | Calculate the percentage of spiked species retrieval | spiked species retrieval is system-dependent | Spiked species and related parameters for ITS | Calculating Scaling Factors | Convert relative counts to absolute counts | Summary Stat | Conclusion | Abundance-based Core microbiome | Data transform & Normalization | Ridge plot | Differential abundance (Single Pairwise) | Differential abundance (Multilayer Pairwise) | Turnover (Presence/absence analysis) | Visualization | Microbial dynamics & NetWork comparision | Visualizes pairwise relationships between node-level metrics using a quadrant-based plot | Comparision of node-level metrics | To find neighbors of the target node | Compute degree metrics and visualize the network | Small-World Index Analysis | DspikeIn volume protocol