NEWS.md

mizerMR (development version)

• The resources can now be balanced, as mizer's single resource has always been: setMultipleResources() gained a resource_level argument and a balance argument, and there are new resource_level() and resource_level<-() accessors. Giving exactly one of resource_rate, resource_capacity or resource_level now by default determines the other one from the requirement that each resource replenishes at exactly the rate at which it is consumed, so that the current resource abundances are a steady state. Each resource is balanced with the balancing function belonging to its own dynamics, and resources whose dynamics has no such function are left alone. Pass balance = FALSE to switch this off, for example resource_capacity(params, balance = FALSE) <- capacity. The balancing is also available on its own as balanceResources().

• tuneSteadyState() now balances the resources of a multiple-resource model automatically. They are held at their stored abundances while the consumer spectra are solved for, exactly as mizer holds its own resource, and afterwards their capacities are derived from their rates so that those held abundances are a steady state of the resource dynamics under the new spectra. The model you get back is therefore at a fixed point of the resource dynamics as well as of the consumer dynamics, and mizer no longer reports the MR component as one it is holding fixed without being able to handle.

• setMultipleResources() gained a reset argument that recalculates the resource rate and capacity from the resource parameters even if they were previously set by hand or by balancing.

• mizerMR now requires mizer (>= 3.3.0) and follows the plotting interface that mizer introduced in that release. plotSpectra() and animate() take the biomass and per_log_size flags, whose sum is the power of the weight multiplying the number density; power is still accepted and is the only way to ask for a power that is not such a sum, but a power that contradicts the flags is now an error rather than being silently resolved.

• plotSpectra(), animate() and the plot() methods of the resource array classes now honour size_axis = "l", llim, log_x, log_y and log, which used to be ignored. On a length axis the resources are converted with the weight-length relationship mizer uses for its own resource (a and b from resource_params(), or mizer's defaults), which is the same one with which the combined resource enters the total, and a density picks up the dw/dl Jacobian. The total is summed on the axis it is plotted against. plotSpectra() also honours resource = FALSE and now labels its axes and places its legend exactly as mizer does.

• The resource arrays returned by initialNResource(), NResource(), finalNResource() and getResourceMort() carry mizer's new type attribute saying what kind of quantity they hold, and their plot() method uses it: a density can be converted to a length axis or shown per logarithmic size, a rate cannot, and a proportion would be drawn on a linear axis from 0 to 1. MRArrayResourceBySize() and MRArrayTimeByResourceBySize() gained a type argument.

• plotDiet() honours size_axis, wlim, llim, log_x and log_y, which used to be ignored. Its wlim default is now c(NA, NA) as in mizer, rather than the c(1, NA) that never took effect.

• plotResourceLevel() shows the whole of the interval from 0 to 1 on its y axis, as mizer now does for a proportion.

• newMRParams() and setMultipleResources() gained an info_level argument and report through mizer's reporting mechanism, so that everything mizerMR says while building or changing a model obeys info_level and arrives together with mizer's own reports at the end of the call.

• mizerMR now respects mizer's second_order_w flag. When second-order bin-averaging is switched on, each resource's carrying capacity and replenishment rate are built from the exact bin averages of their power laws over the resource's size range (with the bins straddling w_min/w_max getting the partial average) rather than point-sampled at the left bin edge, and the initial resource inherits the bin-averaged capacity. newMRParams() gains a second_order_w argument that is passed through to mizer's constructor. The default (first-order) behaviour is unchanged and the package still works against mizer versions without the second_order_w slot.

• The resource accessors (getResourceMort(), initialNResource(), finalNResource() and NResource()) now return classed objects (MRArrayResourceBySize and MRArrayTimeByResourceBySize) that support print(), summary(), plot() and as.data.frame() methods, so you can do e.g. plot(getResourceMort(params)) or plot(NResource(sim)) with one coloured line per resource. This mirrors the corresponding classes added for the single resource in mizer. Requires mizer (>= 3.0.0.9002).

mizerMR 0.3.0

• Compatible with mizer version 3.0.0
• setMultipleResources() now uses mizer's extension-chain methods for encounter and resource mortality instead of replacing entries in params@rates_funcs, allowing composition with other extension packages.
• Accessors and plots that need multiple-resource behaviour are now registered as methods for mizer's generics. plotlySpectra() has been removed.
• The resource encounter rate is now computed with a single Fourier transform for all resources combined instead of one per resource, so the encounter cost no longer grows with the number of resources. A per-resource fallback is retained for models with a custom (non-Fourier) predation kernel.
• scaleModel(), scaleRates(), setResource() and summary() now have multiple-resource methods. scaleModel() and scaleRates() rescale all resource capacities, abundances and rates consistently (previously scaleModel() errored); setResource() warns that it only affects the silenced built-in resource; and summary() reports the combined resource size range instead of the empty built-in resource.

mizerMR 0.0.3

• plotSpectra() and plotlySpectra() work with multiple resources.
• New plotting functions plotResourceLevel() and plotResourcePred().
• setMultipleResources() no longer changes the initial resource abundances unless supplied via initial_resource.
• Fix bug preventing resource_params() from changing the resource arrays.
• plotDietMR() renamed to plotDiet().

mizerMR 0.0.2

• setMultipleResources() now adds to the extensions field in params metadata.
• plotDietMR() is a replacement for plotDiet() that works with multiple resources.
• setMultipleResources()now sets the inital_n_ppslot to zero so that there are no spurious contributions to getDiet() for example.
• The functions extracting information from MizerParams or MizerSim objects now all fall back onto core mizer functions when called with objects for which no multiple resources have been set up.
• The resource params are now saved in the @other_params slot instead of the resource_params slot to avoid breaking core mizer code.

mizerMR 0.0.1

• First functional version of package, ready for testing.