Man pages for mizer
Multi-Species sIZE Spectrum Modelling in R

BevertonHoltRDDBeverton Holt function to calculate density-dependent...
box_pred_kernelBox predation kernel
compareParamsCompare two MizerParams objects and print out differences
constantEggRDIChoose egg production to keep egg density constant
constant_otherHelper function to keep other components constant
constantRDDGive constant reproduction rate
customFunctionReplace a mizer function with a custom version
default_pred_kernel_paramsSet defaults for predation kernel parameters
differentCheck whether two objects are different
distanceMaxRelRDIMeasure distance between current and previous state in terms...
distanceSSLogNMeasure distance between current and previous state in terms...
double_sigmoid_lengthLength based double-sigmoid selectivity function
emptyParamsCreate empty MizerParams object of the right size
finalNSize spectra at end of simulation
finalNOtherValues of other ecosystem components at end of simulation
gear_paramsGear parameters
getBiomassCalculate the total biomass of each species within a size...
getBiomassFrameGet data frame of biomass of species through time, ready for...
getCommunitySlopeCalculate the slope of the community abundance
getComponentGet information about other ecosystem components
getCriticalFeedingLevelGet critical feeding level
getDietGet diet of predator at size, resolved by prey species
getEffortFishing effort used in simulation
getEGrowthGet energy rate available for growth
getEncounterGet encounter rate
getEReproGet energy rate available for reproduction
getEReproAndGrowthGet energy rate available for reproduction and growth
getESpawningAlias for getERepro
getFeedingLevelGet feeding level
getFMortGet the total fishing mortality rate from all fishing gears...
getFMortGearGet the fishing mortality by time, gear, species and size
get_gamma_defaultGet default value for gamma
getGrowthCurvesGet growth curves giving weight as a function of age
get_h_defaultGet default value for h
get_initial_nCalculate initial population abundances for the community...
get_ks_defaultGet default value for 'ks'
getM2Alias for getPredMort
getM2BackgroundAlias for getResourceMort
getMeanMaxWeightCalculate the mean maximum weight of the community
getMeanWeightCalculate the mean weight of the community
getMortGet total mortality rate
getNCalculate the number of individuals within a size range
getParamsExtract the parameter object underlying a simulation
get_phiGet values from feeding kernel function
getPhiPreyGet available energy
getPredKernelGet predation kernel
getPredMortGet total predation mortality rate
getPredRateGet predation rate
getProportionOfLargeFishCalculate the proportion of large fish
getRatesGet all rates
getRDDGet density dependent reproduction rate
getRDIGet density independent rate of egg production
get_required_reproductionDetermine reproduction rate needed for initial egg abundance
getResourceMortGet predation mortality rate for resource
get_size_range_arrayGet size range array
getSSBCalculate the SSB of species
get_time_elementsGet_time_elements
getTimesTimes for which simulation results are available
getYieldCalculate the total yield of each species
getYieldGearCalculate the total yield per gear and species
getZAlias for getMort
idxFinalTTime index at end of simulation
indicator_functionsDescription of indicator functions
initialNOther-setInitial values for other ecosystem components
initialNResource-setInitial value for resource spectrum
initialN-setInitial values for fish spectra
interExample interaction matrix for the North Sea example
knife_edgeWeight based knife-edge selectivity function
log_breaksHelper function to produce nice breaks on logarithmic axes
lognormal_pred_kernelLognormal predation kernel
mizerEGrowthGet energy rate available for growth needed to project...
mizerEncounterGet encounter rate needed to project standard mizer model
mizerEReproGet energy rate available for reproduction needed to project...
mizerEReproAndGrowthGet energy rate available for reproduction and growth needed...
mizerFeedingLevelGet feeding level needed to project standard mizer model
mizerFMortGet the total fishing mortality rate from all fishing gears
mizerFMortGearGet the fishing mortality needed to project standard mizer...
mizerMortGet total mortality rate needed to project standard mizer...
mizer-packagemizer: Multi-species size-based modelling in R
MizerParamsAlias for set_multispecies_model
MizerParams-classA class to hold the parameters for a size based model.
mizerPredMortGet total predation mortality rate needed to project standard...
mizerPredRateGet predation rate needed to project standard mizer model
mizerRatesGet all rates needed to project standard mizer model
mizerRDIGet density-independent rate of reproduction needed to...
mizerResourceMortGet predation mortality rate for resource needed to project...
MizerSimConstructor for the 'MizerSim' class
MizerSim-classA class to hold the results of a simulation
NTime series of size spectra
newCommunityParamsSet up parameters for a community-type model
newMultispeciesParamsSet up parameters for a general multispecies model
newTraitParamsSet up parameters for a trait-based model
noRDDGive density-independent reproduction rate
NOtherTime series of other components
NS_paramsExample MizerParams object for the North Sea example
NS_species_paramsExample species parameter set based on the North Sea
NS_species_params_gearsExample species parameter set based on the North Sea with...
plotBiomassPlot the biomass of species through time
plotDietPlot diet
plotFeedingLevelPlot the feeding level of species by size
plotFMortPlot total fishing mortality of each species by size
plotGrowthCurvesPlot growth curves giving weight as a function of age
plotM2Alias for plotPredMort
plotMizerSimSummary plot for 'MizerSim' objects
plotPredMortPlot predation mortality rate of each species against size
plotSpectraPlot the abundance spectra
plotting_functionsDescription of the plotting functions
plotYieldPlot the total yield of species through time
plotYieldGearPlot the total yield of each species by gear through time
power_law_pred_kernelPower-law predation kernel
projectProject size spectrum forward in time
project_simpleProject abundances by a given number of time steps into the...
projectToSteadyProject to steady state
reexportsObjects exported from other packages
resource_constantKeep resource abundance constant
resource_paramsResource parameters
resource_semichemostatProject resource using semichemostat model
retune_ereproRetune reproduction efficiency to maintain initial egg...
RickerRDDRicker function to calculate density-dependent reproduction...
setBevertonHoltSet Beverton-Holt density dependence
setColoursSet line colours to be used in mizer plots
set_community_modelDeprecated function for setting up parameters for a...
setComponentAdd a dynamical ecosystem component
setExtMortSet external mortality rate
setFishingSet fishing parameters
setInitialValuesSet initial values to final values of a simulation
setInteractionSet species interaction matrix
setLinetypesSet linetypes to be used in mizer plots
setMaxIntakeRateSet maximum intake rate
setMetabolicRateSet metabolic rate
set_multispecies_modelDeprecated obsolete function for setting up multispecies...
setParamsSet or change any model parameters
setPredKernelSet predation kernel
setRateFunctionSet own rate function to replace mizer rate function
setReproductionSet reproduction parameters
setResourceSet up resource
setRmaxAlias for setBevertonHolt
setSearchVolumeSet search volume
set_species_param_defaultSet a species parameter to a default value
set_trait_modelDeprecated function for setting up parameters for a...
SheperdRDDSheperd function to calculate density-dependent reproduction...
sigmoid_lengthLength based sigmoid selectivity function
sigmoid_weightWeight based sigmoidal selectivity function
species_paramsSpecies parameters
steadySet initial values to a steady state for the model
summary_functionsDescription of summary functions
summary-MizerParams-methodSummarize MizerParams object
summary-MizerSim-methodSummarize MizerSim object
truncated_lognormal_pred_kernelTruncated lognormal predation kernel
upgradeParamsUpgrade MizerParams object from earlier mizer versions
upgradeSimUpgrade MizerSim object from earlier mizer versions
validEffortVectorReturn valid effort vector
validGearParamsCheck validity of gear parameters and set defaults
validParamsValidate MizerParams object and upgrade if necessary
valid_species_argHelper function to assure validity of species argument
validSpeciesParamsValidate species parameter data frame
wSize bins
mizer documentation built on March 21, 2021, 5:07 p.m.