Package index

Setting multiple resources

resource_params() `resource_params<-`()

Resource parameters

setMultipleResources() resource_capacity() `resource_capacity<-`() resource_rate() `resource_rate<-`() resource_interaction() `resource_interaction<-`() initialNResource(<mizerMR>) `initialNResource<-`(<mizerMR>)

Set up multiple resources

newMRParams()

Create a new multi-resource, multi-species model

Accessing results of simulations

NResource(<mizerMRSim>) finalNResource(<mizerMRSim>)

Access resource abundances in simulation result

plotSpectra(<mizerMRSim>) plotSpectra(<mizerMR>)

Plot the abundance spectra

getDiet(<mizerMR>)

Get diet of predator at size, resolved by prey species

plotDiet(<mizerMR>) plotDiet(<mizerMRSim>) plotDietMR() experimental

Plot diet, resolved by prey species, as function of predator at size.

plotResourceLevel()

Plot the proportion of the resource spectrum(s) compared to their carrying capacity

plotResourcePred() plotlyResourcePred()

Plot functions regarding the resources. Compatible with non mizerMR objects Plot the mortality applied on the resource spectrum(s)

animateSpectra.mizerMRSim() experimental

Animation of the abundance spectra

scaleModel(<mizerMR>) scaleRates(<mizerMR>) setResource(<mizerMR>) summary(<mizerMR>)

Multiple-resource methods for model rescaling and reporting

MRArrayResourceBySize()

S3 class for multiple-resource size spectra

MRArrayTimeByResourceBySize()

S3 class for time x resource x size arrays

is.MRArrayResourceBySize()

Test if an object is an MRArrayResourceBySize

is.MRArrayTimeByResourceBySize()

Test if an object is an MRArrayTimeByResourceBySize

plot(<MRArrayResourceBySize>) plotHover(<MRArrayResourceBySize>) plot(<MRArrayTimeByResourceBySize>) plotHover(<MRArrayTimeByResourceBySize>)

Plot mizerMR resource arrays

Species utilities

addSpecies(<mizerMR>)

Add species to a mizerMR model

removeSpecies(<mizerMR>)

Remove species from a mizerMR model

renameSpecies(<mizerMR>)

Rename species in a mizerMR model

expandSizeGrid(<mizerMR>)

Expand the size grid of a mizerMR model

Internal helper functions

validResourceParams()

Validate resource parameter data frame

valid_resources_arg()

Helper function to assure validity of resources argument

set_resource_param_default()

Set a resource parameter to a default value

mizerMR-class mizerMRSim-class

mizerMR marker classes

mizerMRBaseResource() mizerMRValidBaseResource() getEncounter(<mizerMR>) getPredRate(<mizerMR>) getResourceMort(<mizerMR>) getRates(<mizerMR>) projectEncounter(<mizerMR>) mizerMREncounter() mizerMRResourceEncounter() projectResourceMort(<mizerMR>)

Multiple-resource project methods

mizerMR_dynamics()

Multiple-resource dynamics

plotDietData()

Format and plot MR diet data

expect_unchanged()

Expect a mizer object to be unchanged

.onLoad()

Register mizerMR with mizer

.strip_mr()

Strip the MR extension from params