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mizer 2.5.0

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@gustavdelius gustavdelius released this 08 Dec 17:42
· 57 commits to master since this release
v2.5.0
ab717fe

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:

  • Part 1: Understand
    You will gain an understanding of size spectra and their dynamics by exploring simple example systems hands-on with mizer.

  • Part 2: Build
    You will build your own multi-species mizer model for the Celtic sea, following our example. You can also create a model for your own area of interest.

  • Part 3: Use
    You will explore the effects of changes in fishing and changes in resource dynamics on the fish community and the fisheries yield. You will run your own model scenarios.

Other improvements

  • Warnings are given if user gives irrelevant species parameter values.
  • Some messages have been converted to warnings and some to signals that are not
    shown as frequently.
  • Frequent warnings are avoided when length-based and weight-based parameters
    are both given and are inconsistent. #277
  • Documentation of effort argument in project() is improved.
  • An error message is given if a predation kernel returns negative values or
    is everywhere zero. #283

Bug fixes

  • When the coefficient h of the maximum intake rate is not given, it is now
    again given a default value. #282
  • matchGrowth() no longer gives an error when there is no w_inf column. #279
Assets 2