The process of building a new multi-species model by adding the species to a generic trait-based background has better support.
tuneParams() starts a shiny gadget that allows for interactive tuning of model parameters while various plots update automatically.addSpecies() can now add several species at once, all at low abundancepruneSpecies(), renameSpecies(), rescaleAbundance(), retuneReproductionEfficiency().retuneBackground(), Singular Value Decomposition is used to retune background species to keep the community close to power law. Background species with very low abundances are automatically removed.setRmax().After setting up a mizer model, it is possible to change specific model parameters with the new functions
setPredKernel()setSearchVolume()setInteraction()setIntakeMax()setMetab()setBMort()setReproduction()setFishing()setPlankton()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)
plotlyBiomass() as the plotly version of plotBiomass(), and so on.plotGrowthCurves() plots growth curves and compares them to the von Bertalanffy growth curve.plotDiet() plots the diet composition as a function of predator size.highlight argument to all plot functions that display curves for multiple species. Displays highlighted species with wider lines.plot() method for MizerParams object to plot the initial state.print_it argument in plot functions to FALSE.wlim argument to plotSpectra() in analogy to the existing ylim argument to limit the w range in the plot.xlab and ylab for displayFrames().linecolour slot.solid but this can be changed via the linetype slot.box_pred_kernel() implements a box-shaped kernel as an alternative to the default lognormal_pred_kernel().power_law_pred_kernel() implements a power-law kernel with sigmoidal cutoffs at both ends. This is suitable for filter feeders.setPredKernel()). Mizer automatically falls back on the old non-FFT code to handle this. (#41)getPredKernel() returns the full 3-dimensional predation kernel array, even when this is not stored in MizerParams object.fc can now be specified as a species parameter and will be used to calculate the metabolic rate parameter ks if it is not supplied.newSheldonParams() that sets up a single species in a power-law background.upgradeParams() can upgrade MizerParams objects from previous versions of mizer so they work with the new version.project() now shows a progress bar while a simulation is running. Can be turned off with progress_bar = FALSE argument.getDiet() calculates the diet of predators. (#43)srrRicker() and srrSheperd().Inf.plankton_semichemostat().interaction_p column in the species parameter data frame.double_sigmoid_length() allows modelling of escape of large individuals.sigmoidal_weight() is weight-based trawl selectivity function. (Ken H Andersen)w_mat25 column in the species parameter dataframe, which gives the size at which 25% of the individuals of a species are mature.m column in the species parameter data frame.project() can now continue projection from last time step of a previous simulation if the first argument is a MizerSim object. The new append argument then controls whether the new results are appended to the old.getGrowthCurves() calculates the growth curves (size at age).newMultispeciesParams().getRates() calculates all the rates needed in the model and collects them in a list.setInitial().initial_n, initial_n_pp and initial_B arguments from the corresponding slot in the params argument.perfect_scaling argument allows newTraitParams() to produce a perfectly scale-invariant model.bmort_prop argument in newTraitParams() allows the inclusion of background death.newMultispeciesParams().getmM2() -> getPredMort()
plotM2 -> plotPredMort()
getM2background() -> getPlanktonMort()
getZ() -> getMort()
getESpawning() -> getERepro()
MizerParams() -> emptyParams() or set_multispecies_model()
Added ecosystems from N.S. Jacobsen, M. Burgess and K.H. Andersen (2017): Efficiency of fisheries is increasing at the ecosystem level. Fish and Fisheries 18(2) 199- 211. doi:10.1111/faf.12171:
data(Benguela_params) with five species: Anchovy, Sardine, Kingklip, Shallow water hake, and Deep water hake.data(Baltic_params) with three species: sprat, herring, and cod.data(Barents_params) with six species.data(NEUSCS_params) with 24 species.data(NorthSea_params) with 10 species.getSSB(), the calculation of the spawning stock biomass is done correctly using the maturity ogive instead of the proportion of energy allocated to reproduction. (#47)getEncounter() and getPredRate() now set names on the returned arrays.ylim argument is not handled correctly in plots.display_frame() is now exported.get_gamma_default(), get_h_default() and get_ks_default(), making it easier to change or extend these in the future.set_species_param_default() makes it easier to set default values for species parameters.@inherit functionality of roxygen2 to reduce duplication in roxygen documentation.getPhiPrey() is replaced by getEncounter() which now returns the full encounter rate, including the contribution from other components. Even in the absence of other components, getEncounter() differs from the old getPhiPrey() because it includes the search volume factor.params to refer to an argument of class MizerParams, sim to refer to an argument of class MizerSim, and object to an argument that can be either.setClass() to follow the new guidelines, replacing representation by class and removing prototype and validity.shiny_progress renamed to progress_bar because they control any type of progress bar.outer() instead of tapply() where possible to improve readability.hasArg() and anyNA() because they were not available in R 3.1std_metab and activity slots into a single metab slot.w_min_idx out of species_params into its own slot.maturity to hold the maturity ogive.pred_kernel to hold predation kernel if it has variable predator/prey ratio.plankton_dynamics to allow user to specify alternative plankton dynamics.srr to hold the name of the stock recruitment function rather than the function itself, see #91.print_it argument from plot functions.all.sizes = TRUE.set_scaling_model(), see section 12 in the vignette.PlotYield() no longer fails when species names are numbers or when a species abundance is zerototal parameter to several plot functions to add the curve for the total community (sum over all species and plankton)species parameter to all plot functions to allow for only a selection of species to be plottedgetPhiPrey() and getPredRate().getPhiPrey() and getPredRate().