mizer-package |
mizer: Multi-species size-based modelling in R |
addSpecies |
Add more species into an ecosystem with background species. |
addSpecies-method |
Add more species into an ecosystem with background species. |
display_frames |
Display frames |
getBiomass |
Calculate the total biomass of each species within a size range at each time step. |
getBiomass-method |
Calculate the total biomass of each species within a size range at each time step. |
getBiomassFrame |
Get data frame of biomass of species through time, ready for ggplot2 |
getBiomassFrame-method |
Get data frame of biomass of species through time, ready for ggplot2 |
getCommunitySlope |
Calculate the slope of the community abundance |
getCommunitySlope-method |
Calculate the slope of the community abundance |
getEGrowth |
Get energy rate available for growth |
getEGrowth-method |
Get energy rate available for growth |
getEReproAndGrowth |
Get energy after metabolism and movement |
getEReproAndGrowth-method |
Get energy after metabolism and movement |
getESpawning |
Get energy rate available for reproduction |
getESpawning-method |
Get energy rate available for reproduction |
getFeedingLevel |
Get feeding level |
getFeedingLevel-method |
Get feeding level |
getFMort |
Get the total fishing mortality rate from all fishing gears by time, species and size. |
getFMort-method |
Get the total fishing mortality rate from all fishing gears by time, species and size. |
getFMortGear |
Get the fishing mortality by time, gear, species and size |
getFMortGear-method |
Get the fishing mortality by time, gear, species and size |
getM2 |
getM2 method for the size based model |
getM2-method |
getM2 method for the size based model |
getM2Background |
Get predation mortality rate for plankton |
getM2Background-method |
Get predation mortality rate for plankton |
getMeanMaxWeight |
Calculate the mean maximum weight of the community |
getMeanMaxWeight-method |
Calculate the mean maximum weight of the community |
getMeanWeight |
Calculate the mean weight of the community |
getMeanWeight-method |
Calculate the mean weight of the community |
getN |
Calculate the total abundance in terms of numbers of species within a size range |
getN-method |
Calculate the total abundance in terms of numbers of species within a size range |
getPhiPrey |
Get available energy |
getPhiPrey-method |
Get available energy |
getPredRate |
Get predation rate |
getPredRate-method |
Get predation rate |
getProportionOfLargeFish |
Calculate the proportion of large fish |
getProportionOfLargeFish-method |
Calculate the proportion of large fish |
getRDD |
Get density dependent recruitment |
getRDD-method |
Get density dependent recruitment |
getRDI |
Get density independent recruitment |
getRDI-method |
Get density independent recruitment |
getSSB |
Calculate the SSB of species |
getSSB-method |
Calculate the SSB of species |
getSSBFrame |
Get data frame of spawning stock biomass of species through time, ready for ggplot2 |
getSSBFrame-method |
Get data frame of spawning stock biomass of species through time, ready for ggplot2 |
getYield |
Calculate the total yield of each species |
getYield-method |
Calculate the total yield of each species |
getYieldGear |
Calculate the total yield per gear and species |
getYieldGear-method |
Calculate the total yield per gear and species |
getZ |
Get total mortality rate |
getZ-method |
Get total mortality rate |
get_initial_n |
Calculate initial population abundances for the community populations |
inter |
Example interaction matrix for the North Sea example |
knife_edge |
Size based knife-edge selectivity function |
log_breaks |
Helper function to produce nice breaks on logarithmic axes |
mizer |
mizer: Multi-species size-based modelling in R |
mizer, |
mizer: Multi-species size-based modelling in R |
MizerParams |
Constructors for objects of 'MizerParams' class |
MizerParams-class |
A class to hold the parameters for a size based model. |
MizerParams-method |
Constructors for objects of 'MizerParams' class |
MizerSim |
Constructor for the 'MizerSim' class |
MizerSim-class |
MizerSim |
MizerSim-method |
Constructor for the 'MizerSim' class |
NS_species_params |
Example parameter set based on the North Sea |
NS_species_params_gears |
Example parameter set based on the North Sea with different gears |
plot-method |
Summary plot for 'MizerSim' objects |
plotBiomass |
Plot the biomass of species through time |
plotBiomass-method |
Plot the biomass of species through time |
plotFeedingLevel |
Plot the feeding level of species by size |
plotFeedingLevel-method |
Plot the feeding level of species by size |
plotFMort |
Plot total fishing mortality of each species by size |
plotFMort-method |
Plot total fishing mortality of each species by size |
plotGrowthCurves |
Plot growth curves giving weight as a function of age |
plotGrowthCurves-method |
Plot growth curves giving weight as a function of age |
plotM2 |
Plot predation mortality rate of each species against size |
plotM2-method |
Plot predation mortality rate of each species against size |
plotSpectra |
Plot the abundance spectra |
plotSpectra-method |
Plot the abundance spectra |
plotYield |
Plot the total yield of species through time |
plotYield-method |
Plot the total yield of species through time |
plotYieldGear |
Plot the total yield of each species by gear through time |
plotYieldGear-method |
Plot the total yield of each species by gear through time |
project |
project method for the size based modelling |
project-method |
project method for the size based modelling |
project_methods |
Methods used for projecting |
retune_abundance |
Retunes abundance of background species. |
setBackground |
Designate species as background species |
setBackground-method |
Designate species as background species |
set_community_model |
Sets up parameters for a community-type model |
set_scaling_model |
Sets up parameters for a scale free trait-based model |
set_trait_model |
Sets up parameters for a trait-based model |
sigmoid_length |
Length based sigmoid selectivity function |
steady |
Tune params object to be at steady state |
summary-method |
Summarize MizerParams object |
summary-method |
Summarize MizerSim object |
wrapper_functions |
Functions used for setting up models |