Changes in version 1.6.2 (2025-09-05)                  

Major Changes

  - None

Minor Changes

  - Fixed deposition issues in cubeClvR2() - Thank you Dr. Leftwich.
  - Updated internal documentation - per CRAN requests.
  - Exported several new inheritance patterns that have been in
    development.
  - Updated website documentation, switched to the current version of
    pkgdown.
  - Updated vignette options to reduce package size.

                        Changes in version 1.6.1                        

Major Changes

  - Rebuild of oneDay_mating_deterministic_Patch() and
    oneDay_mating_stochastic_Patch(). They properly account for zero
    probabilities with males and the associated female deaths.
      - This fixes a bug introduced when eta() was turned into a matrix
        object, allowing selective mating.
      - omega() is supposed to be a matrix, and change for each node.
        That isn't implemented here, and I don't know why not.

Minor Changes

  - calcOmega() has been updated internally.
      - A closed-form expression was derived, and the stats::uniroot()
        dependency is removed.
      - This does not actually fix the issue found, which is in the
        bounds for mu.
      - Better bounds-checking was introduced, with a more clear error
        message, to warn users when they encounter this error.

                 Changes in version 1.6.0 (2020-10-05)                  

Major Changes

  - Rebuild of the Migration Function
      - Migration is handled at the Network level now. This removes
        objects from the Patch class, making the package lighter and
        more efficient.
      - Migration is no longer Dirichlet distributed.
  - New Inheritance Patterns
      - One and Two locus Cleave and Rescue (ClvR) constructs have been
        made available.
      - ERACR/eCHACR constructs have been made available.

Minor Changes

  - Spelling checked and errors corrected.
  - Function links in the documentation have been updated.

                 Changes in version 1.5.0 (2020-01-29)                  

Major Changes

  - Complete internal rebuild of MGDrivE implementation.
      - The underlying mathematics are the same, only the implementation
        has been changed.
      - Significant memory reductions.
      - Significant computational reduction.
      - All internal objects and functions have been updated.
      - Most important, the stochastic implementation had a bug in it,
        which has been resolved.
      - All releases are now numeric vectors/matrices indicating the
        genotype and release number; this is handled internally.
      - It is now possible to release mated females.
      - Male-mating ability is now female-genotype dependent, allowing
        for assortative mating.
      - parameterizeMGDrivE() takes several new parameters
          - sampTime indicates how often output is written from the
            simulation
          - inheritanceCube is now required to parameterize the initial
            genotype distributions
          - LarPopRatio, AdPopRatio_F, and AdPopRatio_M have been
            updated internally to reflect accurate default behavior and
            handle different user input to set them.
  - data.table has been removed from the dependencies. This implies
    rebuilds of:
      - splitOutput()
      - aggregateFemales()
      - calcQuantiles()
  - splitOutput() and aggregateFemales() have been fixed to properly use
    the writeDir parameter.

Minor Changes

  - All verbose options have been updated for consistency. The default
    is TRUE.
  - All parameters that previously had to be vectors the same length as
    the number of patches have been updated to take a single number,
    implying that all parameters are the same for each patch, or as a
    vector, so each patch can be specified individually.
  - Plotting functions have been updated to handle any sampling scheme
    (i.e., if output is not written every day).
  - parameterizeMGDrivE() had internal loops replaced with vectorized
    functions.
  - Spelling errors and documentation inconsistencies were addressed.
  - Citation was updated to reflect publication in Methods in Ecology
    and Evolution.

                 Changes in version 1.1.0 (2019-08-19)                  

Major Changes

  - data.table moved to Imports, from Depends.
  - Parameter names made consistent in several auxiliary functions:
      - retrieveOutput()
      - calcQuantiles()
      - plotMGDrivESingle()

Minor Changes

  - Several spelling errors addressed.
  - Realistic landscape example changed to use the zero-inflated kernel,
    instead of the basic exponential kernel.
  - Several plotting tweaks.
  - Added links to the accompanying data analysis package,
    MoNeT-MGDrivE, part of the MoNeT package.