mizer 2.4.0

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

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

• New function steadySingleSpecies() that only balances the size-spectrum
  dynamics while ignoring multi-species effects. In other words, it calculates
  the steady-state size spectrum of each species as it would be if the abundance
  of prey and predators could be kept constant at their current values.
• plotGrowthCurves() can now superimpose a scatterplot of size-at-age data
  if you supply this via the new size_at_age argument.
• New functions calibrateNumber() and matchNumbers() that are like
  calibrateBiomass() and matchBiomasses() but work with observed numbers
  instead of observed biomasses.
• New function age_mat() to calculate the age at maturity from the growth
  rate and the size at maturity.
• If an effort vector or effort array contains NA's, these are now replaced by
  the default effort value. #230
• The entries of the interaction matrix and of interaction_resource are no
  longer restricted to be less or equal to 1. #232
• If user supplies no row names in the interaction matrix but gives column names
  then the column names are also used as row names. #247
• project() now also works when called with a MizerSim object with additional
  components.
• steady() now preserves the RDD function in the MizerParams object rather
  than always setting it to "BevertonHoltRDD".
• When averaging abundances over time in plotSpectra() or setInitialValues()
  the user can now choose geometric averaging with geometric_mean = TRUE.
• The w_mat25 species parameter is no longer filled in automatically if it is
  not supplied. This makes it easier to change w_mat without having to change
  w_mat25 at the same time.
• compareParams() now also checks the validity of its second argument.
• Hide the printing of messages about chosen defaults in newTraitParams().
• Higher values for the info_level argument in newMultispeciesParams() now
  leads to more messages.
• Giving more helpful messages in validSpeciesParams(). #136
• New helper functions l2w() and w2l() for converting between length-based
  and weight-based species parameters. #258
• Check that assessor functions for MizerSim slots are called with a MizerSim
  object.
• Add style argument to plotDataFrame() to facilitate producing area plots.
• Add wrap_scale argument to plotDataFrame() to control scaling of axes in
  faceted plots.
• plotDiet() can now show diets of several predator species in a faceted
  plot. #267
• Change from size to linewidth aesthetic to avoid warnings in new version
  of ggplot2.
• Better error message when functions are called with no valid species selected.
  #251
• If there are no differences then compareParams() says so clearly.
• getReproductionLevel() works as long as R_max is set. #252
• Converted several unit tests to edition 3 of testthat package.
• Improved documentation for gear_params().
• Improved defaults can now be implemented while keeping backwards compatibility
  via defaults_edition(). #186
• New defaults edition 2: catchability = 0.3 instead of 1, initial effort = 1
  instead of 0. #243
• In defaults edition 2, get_gamma_default() ensures a feeding level of f0
  for larvae also if interaction_resource is not equal to 1. #238
• Set default linecolour and linetype for external mortality.

Bug fixes

• Restored the line colours to NS_params
• Comment field now preserved by set_species_default(). #268
• Comment on w_inf no longer leads to error in plyr::aaply(). #269
• Can now again set url field in metadata.
• Correct species now listed in the legend of plotYieldObservedVsModel() and
  plotBiomassObservedVsModel(). #266
• Standard order for legend in plotDiet() restored after change to ggplot2
  package. #265
• Fix handling of column names when interaction matrix is read from .csv file.
  #263