v2.3.0

New features

• New plots plotBiomassObservedVsModel() and plotYieldObservedVsModel()
  contributed by @SamikDatta., together with their plotly counterparts.
• New calibrateBiomass(), calibrateYield() to set the model scale to agree
  with total observed biomass or total observed yield. Uses the new
  scaleModel().
• New matchBiomasses() and matchYields() will try to adjust the abundances
  of the species to produce the observed biomasses or yields.
  See blog post at https://bit.ly/2YqXESV .
• There are now accessor and replacement functions for rates. So for example
  instead of params <- setReproduction(params, maturity = my_maturity) one
  can simply use maturity(params) <- my_maturity. These are documented
  together with the setter functions. #213
• New setMetadata() to add information to a MizerParams object describing
  the model, for example a title, a description, the author or list of
  authors, a url and a doi. This will be particularly useful for sharing your
  models with others
• New saveParams() for saving a MizerParams object to a file and
  readParams() for reading it back in. The resulting files can be shared
  with others who want to run your model.
• A MizerParams object now registers the mizer version under which the model was
  last saved. Should the model not be working as expected in the current version
  of mizer, you can go back to the older version under which presumably it was
  working. This helps with the reproducibility of your research.
• A MizerParams object registers the time when it was created and the time it
  was last modified. See getMetadata(). This helps you keep track of
  different versions of your model.
• steady() now has a preserve argument with possible values erepro,
  R_max or reproduction_level to specify which quantity to preserve.
  This means that one can continue to use steady() also
  once one has started to tune the density dependence in reproduction. #208
• Our website is now using the nice new mizer logo designed by Kira Askaroff
  (www.kiraaskaroff.com)
• There is a new mizer extension package
  mizerMR
  allowing you to include multiple resource spectra in your model.

Small improvements

• The rownames of gear_params are now set to "species, gear", so that one
  can access individual entries with for example
  gear_params(NS_params)["Cod, Otter", "catchability"]. #212
• The z0 argument of setExtMort() has been deprecated in favour of
  ext_mort in order to avoid confusion with the species parameter z0.
• setColours() and setLinetypes() now issue warnings when invalid values
  are given and ignores NAs.
• The experimental comment arguments to the setter functions have been
  removed. #214
• The setter functions have a new reset argument which, when set to TRUE
  will recalculate the rates from the species_, gear_ and resource_params even
  when custom values had been set. #214
• The species argument to various functions, which is checked with
  valid_species_arg(), now does not throw an error even when there is no
  valid species included. Only a warning is issued. That means that for
  example plotSpectra(NS_params, species = list(), total = TRUE) is now
  allowed.
• getComponent() from the mizer extension mechanism now returns NULL when
  asked for a non-existent component instead of giving an error. This gives
  an easy way to check for the existence of a component.
• The example interaction matrix inter for the North Sea model now has the
  alternative name NS_interaction, with the old name deprecated.
• Species added with addSpecies() are now by default given a reproduction
  level of 1/4 instead of 0, because at the low densities at which they are
  introduced there would otherwise not be enough density dependence to
  stabilise them.
• The size range arguments min_w, max_w, min_l and max_l used in some
  summary functions and processed by get_size_range_array() accept vector
  values setting different limits for different species.
• The resource dynamics function is now also passed the resource_rate and the
  resource_capacity as arguments, which makes it easier to use them in
  extension packages.
• Species names are now always coerced to strings, even if the user gives them
  as numbers. #202
• There is a new system for informing the user about how defaults were set by
  newMultispeciesParams(), #199
• Many improvements in the documentation.
• Many small improvements to code quality and testing.
• Better social media cards, especially for twitter.
• mizer can be run on binder, https://mybinder.org/v2/gh/sizespectrum/mizer/HEAD?urlpath=rstudio

Bug fixes

• Changing linecolour or linetype in the species parameters now actually
  changes the linecolours and linetypes as intended.
• Growth curves calculated with getGrowthCurves() and plotted with
  plotGrowthCurves() are now correct, and no longer extend above the
  asymptotic size.
• plotGrowthCurves() with species_panel = TRUE now respects the species
  argument to only show growth curves for selected species, it works with
  a MizerParams object as well as a MizerSim object, and it shows the panels
  in the correct order. #201
• Reinstated the example .csv files that were missing from the package because
  the vignettes are no longer included.