Changes in version 0.0.6 (2026-04-15)                  

New features

Data and Quantum Encoding

Added curated datasets that support reproducible workflows for quantum
state preparation and Hamiltonian construction in immunometabolic
modeling:

  - data_enc: biomarker panel for 3-qubit angle encoding.
  - data_corr: biomarker pool for Hamiltonian correlation structure.

                 Changes in version 0.0.5 (2025-11-09)                  

New features

Quantum Key Distribution (QKD) Protocols

  - Added full simulation of the BB84 protocol through
    run_bb84_simulation().
    This function models the quantum key distribution process between
    Alice and Bob,
    computing the Quantum Bit Error Rate (QBER) under both perfect
    (secure) and
    eavesdropped (compromised) channels.
  - Added simulation of the E91 (Ekert 1991) entanglement-based protocol
    via
    run_e91_simulation().
    This implementation uses Bell’s inequality (CHSH statistic) to
    determine
    whether the communication channel exhibits quantum behavior (|S|
    > 2) or
    classical (insecure) behavior (|S| ≤ 2).

Interaction and Payoffs Framework

  - Improved integration between Interaction and
    InteractionClassification objects.
  - Enhanced the payoff computation workflow, introducing mse.payoffs()
    for
    evaluating mean squared errors between observed and predicted
    payoffs.
  - Updated internal accessors to reduce direct exposure of object
    internals, ensuring
    cleaner S3 method dispatch and reproducibility.

Documentation and Testing

  - Expanded documentation with detailed Roxygen examples and
    theoretical references
    for both BB84 and E91 protocols.
  - Added reproducible test cases and numerical rounding stability in
    snapshot tests.
  - Improved code consistency and formatting to support reproducible
    builds on CRAN.

                 Changes in version 0.0.4 (2025-05-20)                  

New features

Interaction

  - Added new functionalities to the Interaction class, enhancing its
    capabilities for modeling quantum simulations.

InteractionClassification

  - Added new functionalities to the InteractionClassification class.

Quantum game of phenotypes

  - Added new fubnctionalities to design and simulate quantum games of
    HIV phenotypes