NEWS

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PhysioNetPhysiology 0.3.1

Documentation

• Runnable @examples added or corrected across 9 help pages. Each runs offline in seconds, writes nothing outside tempdir(), and is executed by R CMD check; anything needing a device, a download or an optional backend is fenced with the reason stated.
• The README's quick start runs as written: it attaches the package, builds its own inputs, and uses only hard dependencies.

PhysioNetPhysiology 0.3.0

Classical graph-topology metrics and community detection for the physiological networks from tdsNetwork() (previously the package had only degree/strength and partition-consuming role metrics; igraph was suggested but unused).

• networkMetrics() computes the standard node-level (degree, strength, weighted clustering, betweenness, closeness, eigenvector centrality, local efficiency) and global (density, transitivity, characteristic path length, global/local efficiency, degree assortativity, modularity) measures. Edge weights are coupling strengths; path-based metrics use 1/weight distances.
• communityDetection() partitions the network (Louvain / fast-greedy / walktrap / leading-eigenvector / infomap) and reports modularity Q. Its membership feeds the existing moduleRoles() / participationCoefficient(), closing the loop those role metrics needed (they required an externally supplied partition).
• smallWorldness() reports the Humphries-Gurney sigma and Telford omega against degree-preserving random and lattice references.
• These delegate the graph algorithms to igraph (an existing Suggests). Verified on known structure: two-block community recovery (Q ~ 0.49), and a Watts-Strogatz graph flagged small-world (sigma > 1) while a random graph is not.

PhysioNetPhysiology 0.2.0

• The Time Delay Stability engine's windowed peak-lag cross-correlation is now implemented in C++ (Rcpp): about 3x faster than the pure-R loop and byte-identical to it (verified in the test suite). This compounds in the surrogate-threshold path, which runs the engine many times.

PhysioNetPhysiology 0.1.0

• Initial release: Network Physiology for the Physio ecosystem.
• timeDelayStability() — the core Time Delay Stability (TDS) engine over a multivariate physiological series (Bashan et al. 2012).
• tdsSurrogateThreshold() — phase-randomised surrogate significance threshold for TDS links.
• tdsNetwork() — thresholded, weighted organ-interaction networks.
• tdsNetworkByState() / tdsReconfiguration() — state-resolved networks and their reconfiguration across physiological states (e.g. sleep stages).
• physioNodeMatrix() — assemble a node matrix of physiological systems.
• Visualisation: plotDelayStability(), plotTDSnetwork(), plotTDSreconfiguration().