MGDrivE 1.1.0

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.

MGDrivE 1.5.0

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.

MGDrivE 1.6.0

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.

MGDrivE 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.

MGDrivE 1.6.2

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.