mizer 2.5.0

This release introduces a change that requires you to upgrade your old MizerParams and MizerSim objects with upgradeParams() or upgradeSim().

External encounter rate

Now the model can include an external encounter rate that represents the rate at which a predator encounters food that is not explicitly modelled. This encounter rate is set with setExtEncounter() or ext_encounter<-() and can be read with getExtEncounter() or ext_encounter(). So this is similar to how external mortality is handled.

Given versus calculated species parameters

You can now use given_species_params() to see the species parameter values that you have explicitly specified and calculated_species_params() to see the species parameter values that mizer has calculated automatically or set to defaults. You can continue to use species_params() to get all species parameters, irrespective of whether they were given or calculated.

You can still set parameter values with species_params<-(), but you can also use the stronger given_species_params<-() which not only sets the values you give but also triggers a re-calculation of the calculated species parameters. Using given_species_params<-() is therefore usually the better option.

New mizer course

There is now a three-part mizer course at https://mizer.course.sizespectrum.org with each part consisting of several tutorials, including code and exercises:

Other improvements

Bug fixes

mizer 2.4.1

This minor release was made necessary to keep mizer on CRAN after a unit test failed on macOS 13.3 with version 14.3 of the CLT toolchain.

mizer 2.4.0

This release introduces a change that requires you to upgrade your old MizerParams and MizerSim objects with upgradeParams() or upgradeSim().

See mizer 2.4.0 blog post

Avoid confusion between maximum size and von Bertalanffy asymptotic size

For an explanation see blog post at https://blog.mizer.sizespectrum.org/posts/2022-11-30-dont-use-von-bertalanffy-growth-parameters/

The species parameter that specifies the size at which also the largest fish stop growing is renamed from w_inf to w_max. The parameter w_inf is now reserved for the von Bertalanffy asymptotic size parameter. If you upgrade your existing MizerParams object with upgradeParams() the w_inf column is copied over to the w_max column automatically, but you may want to change the values yourself if they do not currently reflect the maximum size of the species. Otherwise the size distributions predicted by mizer will not match observations.

Set resource abundance rather than carrying capacity

The resource parameters kappa and lambda are now used to set the abundance of the resource in the steady state rather than the carrying capacity, because the latter is not observable.

While tuning the steady state using the steady() function the resource abundance is now being kept fixed at the chosen value. Then the resource dynamics can be switched on later with setResource() without changing the steady state. At that stage you only choose either the resource intrinsic growth rate or the resource carrying capacity and the other is determined by setResource() in such a way that the resource replenishes at the same rate at which it is consumed. If you want to keep the old behaviour and switch off this automatic balancing you have to add the balance = FALSE argument when calling setResource().

You can also choose between semichemostat dynamics resource_semichemostat() or logistic dynamics resource_logistic() or you can write your own function implementing more sophisticated resource dynamics.

The setParams() function no longer includes the arguments for setting the resource parameters. Instead you set these separately with setResource().

Automatically match growth rates

As explained in the blog post at https://blog.mizer.sizespectrum.org/posts/2022-11-30-dont-use-von-bertalanffy-growth-parameters/, the von Bertalanffy curves fitted to size-at-age data are not suitable for estimating the size-dependent growth rates in mizer. It is therefore now recommended that instead of von Bertalanffy parameters you supply the age at maturity in the age_mat column of the species parameter data frame. This is then used by mizer to calculate a default for the maximum intake rate parameter h if you do not supply this.

In the past, whenever you changed any model parameters, you needed to re-tune other parameters to keep the growth rates in line with observations. There is now a new function matchGrowth() that automatically scales the search volume, the maximum consumption rate and the metabolic rate all by the same factor in order to achieve a growth rate that allows individuals to reach their maturity size by their maturity age while keeping the feeding level and the critical feeding level unchanged. This function does not however preserve the steady state, so you will need to also call steady() after matching the growth rates.

Other improvements

Bug fixes

mizer 2.3.1

mizer 2.3.0

New features

Small improvements

Bug fixes

mizer 2.2.1

New functionality

Bug fixes

Other improvements

mizer 2.2.0

New functionality

Breaking changes

Bug fixes

Documentation

mizer 2.1.0

New functionality

Breaking changes

Bug fixes

Code improvements

mizer 2.0.4

Bug fixes

Enhancements

mizer 2.0.3

Bug fixes

Enhancements

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