Changes in version 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.

                        Changes in version 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.

                        Changes in version 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.

                        Changes in version 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().