Changelog • mizerSeasonal

mizerSeasonal 0.0.0.9004

Raised the minimum supported mizer version to 3.3.0 and updated the package to use mizer-managed dynamic marker classes and versioned extension metadata.
Upgraded the packaged datta_params model for mizer 3.3.0 and added regression tests for its validity.
Added datta_params_second_order, a separately constructed version of the Datta & Blanchard (2016) model using second_order_w = TRUE and initialised at the steady state of the second-order model.

Converted seasonal reproduction to mizer’s composable extension mechanism. Seasonal reproduction and encounter rates now dispatch through the mizerSeasonal marker class, and the encounter method builds on other mizer extensions with NextMethod().
Added comprehensive tests for extension registration, seasonal dynamics, gonad-release functions, and plotting helpers.
Fixed plotGonadsVsTime() so that selected sizes and time ranges are handled correctly.
Added a vignette describing the package architecture and expanded the theoretical gonadic-mass vignette to cover growth diffusion, finite-volume bin averages, and second-order flux schemes.
Added repository guidance and workflows for coding agents working with mizer extensions.

Updated the package for mizer 2.5.1.
Added and documented datta_params, a MizerParams reconstruction of the base model used by Datta & Blanchard (2016), with its initial state set to the mizer steady state.
Corrected indices in the gonadic-mass derivation and substantially expanded the function, getting-started, and theoretical documentation.
Converted the theoretical vignette to Quarto and refreshed the package website.
Adopted four-space indentation for mizer code in the lint configuration.

Implemented seasonal reproduction by accumulating gonadic mass and releasing it according to a configurable, time-dependent mass-specific release rate.
Added von Mises, beta, beta-hazard, and Gaussian gonad-release functions, and corrected the expression used for the von Mises distribution.
Added time-dependent density-dependent reproduction functions, including seasonal Beverton-Holt and von Mises forms, together with support for finding a steady state while reproduction and resource inputs are held independent of abundance.
Added seasonal semichemostat resource dynamics for modelling resource blooms.
Included the gonadic mass of prey in encounter rates by default, with an option to disable it in setSeasonalReproduction().
Added animateGonadSpectra(), plotRDI(), plotRDD(), plotGonadsVsTime(), and getTimeseries() for inspecting simulations.
Added getting-started examples based on the North Sea model and a vignette deriving the gonadic-mass dynamics.
Published the first pkgdown website and added spelling and build checks.

Created the package and began the first implementation of pulsed and seasonal reproduction.
Added the gonad component and its dynamics for accumulating reproductive investment between spawning events.
Added the initial package documentation and build configuration.