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@gustavdelius gustavdelius released this 17 Oct 16:10
· 11 commits to master since this release
v2.5.3
3da047f

This is a patch release with many small fixes and improvements since the v2.5.0 release.

  • validSpeciesParams() has extra checks on consistency of species parameters.
  • validParams() checks that rate arrays contain finite numeric values.
  • validSim() checks that simulation results are finite and truncates the
    simulation if they are not.
  • Fixed bug that had led newCommunityParams() to set up resource parameters
    differently since version 2.4.0 (#293).
  • addSpecies() now correctly preserves all species_params of the existing
    model.
  • addSpecies() no longer requires new species to grow to maximum size, only
    maturity size is required.
  • Now validGivenSpeciesParams() validates the given species parameters without
    adding defaults and validSpeciesParams() validates and returns a completed
    species parameter dataframe.
  • New species parameter w_repro_max giving the size at which a species
    invests 100% of its energy into reproduction. Set to w_max by default.
  • removeSpecies() now also removes species parameters that are NA for
    all of the remaining species.
  • Changing w_max now also correctly updates ft_mask (#296).
  • compareParams() now also spells out differences in given species parameters.
  • getDiet() now also includes the contribution of the external encounter rate
    to the diet.
  • setPredKernel() now throws an error if some of the required predation kernel
    parameters are NA.
  • In plotYieldGear() one can select a subset of gears with a new gears
    argument.
  • New helper function valid_gears_arg() to check the gears argument in
    functions that take a gears argument.
  • Improved scaling of the y-axis in plotGrowthCurves().
  • steadySingleSpecies() no longer requires species to grow to w_max.
  • matchGrowth() now also rescales the external encounter rate.
  • setExtEncounter() no longer resets the external encounter rate to zero when
    called without the ext_encounter argument.
  • The function plotBiomassObservedVsModel() now plots the ratio of modelled
    to observed biomass as default (ratio = TRUE).
  • The time_modified field is now updated correctly by steadySingleSpecies(),
    setColours() and setLinetypes().
  • Deprecated matchYields() and calibrateYield().
  • project() and projectToSteady(..., return_sim = TRUE) now correctly
    returns also the other components of the MizerSim object stored in n_other.
    #285
  • Improved some unit tests.
  • Some improvements to documentation.
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