mizer 2.0.2

Bug fixes

Name changes

Minor enhancements

mizer 2.0.1

Bug fixes

Name changes

Some inconsistencies in the choice of names for parameters was removed by renaming

Minor enhancements

mizer 2.0.0

This is a major new release with many new features, an internal refactoring of the code and a new extension mechanism.

Backwards compatibility

Nevertheless this version of mizer is almost fully backwards compatible with version 1.0 with the exception of bug fixes and the following breaking changes:

Setting up models

The new functions

replace the old functions set_community_model(), set_trait_model() and MizerParams(), which are now deprecated. The new functions choose better default values, in particular for metabolic rate and maximum intake rate.

Setting model parameters

After setting up a mizer model, it is possible to change specific model parameters with the new functions

The new function setParams() is a wrapper for all of the above functions and is also used when setting up a new model with newMultispeciesParams(). (#51)

The documentation for these functions serves to explain the details of the mizer model.

Along with these setter functions there are accessor functions for getting the parameter arrays: getPredKernel(), getSearchVolume(), getInteraction(), getMaxIntakeRate(), getMetabolicRate(), getExtMort(), getMaturityProportion(), getReproductionProportion(), getCatchability(), getSelectivity(), getResourceRate(), getResourceCapacity(), getResourceParams(), getResourceDynamics(),

Initial Values and steady state

The MizerParams object now also contains the initial values for the size spectra. This is particularly useful if the model has been tuned to produce the observed steady state. The new function steady() finds a steady state for a model and sets it as the initial value. The initial values can be accessed and changed via functions initialN() and initialNResource(). The initial values can be set to the final values of a previous simulation with setInitialValues().

The MizerParams object now has a slot initial_effort that specifies the initial fishing effort to which the steady state has been calibrated.

Extension mechanisms

Mizer now has an extension mechanism that allows other R packages to be written to generalise the mizer model. See setRateFunction() and setComponent(). This mechanism is still experimental and may change as we gain experience in writing extensions for mizer.

Plotting

General predation kernel

New gear setup

Now it is finally possible to have several gears (or fleets) targeting the same species. The information is set up via a new gear_params() data frame. See setFishing() for details.

Other new functions

Other new features

Documentation

Bug fixes

Under the hood

mizer 1.0.1

mizer 1.0

mizer 0.4

mizer 0.3

mizer 0.2

mizer 0.1