Package: mizer 2.5.1.9003

Gustav Delius

mizer: Dynamic Multi-Species Size Spectrum Modelling

A set of classes and methods to set up and run multi-species, trait based and community size spectrum ecological models, focused on the marine environment.

Authors:Gustav Delius [cre, aut, cph], Finlay Scott [aut, cph], Julia Blanchard [aut, cph], Ken Andersen [aut, cph], Richard Southwell [ctb, cph]

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mizer/json (API)
NEWS

# Install 'mizer' in R:

install.packages('mizer', repos = c('https://sizespectrum.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sizespectrum/mizer/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

NS_interaction - Example interaction matrix for the North Sea example
NS_params - Example MizerParams object for the North Sea example
NS_sim - Example MizerSim object for the North Sea example
NS_species_params - Example species parameter set based on the North Sea
NS_species_params_gears - Example species parameter set based on the North Sea with different gears
inter - Alias for 'NS_interaction'

On CRAN:

ecosystem-model fish-population-dynamics fisheries fisheries-management marine-ecosystem population-dynamics simulation size-structure species-interactions transport-equation

253 exports 36 stars 3.53 score 81 dependencies 4 mentions 236 scripts 466 downloads

Last updated 21 days agofrom:ea3ae441ee. Checks:ERROR: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Aug 28 2024
R-4.5-win-x86_64	NOTE	Aug 28 2024
R-4.5-linux-x86_64	NOTE	Aug 28 2024
R-4.4-win-x86_64	NOTE	Aug 28 2024
R-4.4-mac-x86_64	NOTE	Aug 28 2024
R-4.4-mac-aarch64	NOTE	Aug 28 2024
R-4.3-win-x86_64	NOTE	Aug 28 2024
R-4.3-mac-x86_64	NOTE	Aug 28 2024
R-4.3-mac-aarch64	NOTE	Aug 28 2024

Exports:addSpecies age_mat animateSpectra balance_resource_logistic balance_resource_semichemostat BevertonHoltRDD box_pred_kernel calc_selectivity calculated_species_params calibrateBiomass calibrateNumber calibrateYield catchability catchability<-compareParams completeSpeciesParams constant_other constantEggRDI constantRDD customFunction default_pred_kernel_params defaults_edition distanceMaxRelRDI distanceSSLogN double_sigmoid_length dw dw_full emptyParams ext_encounter ext_encounter<-ext_mort ext_mort<-finalN finalNOther finalNResource gear_params gear_params<-get_f0_default get_gamma_default get_h_default get_initial_n get_ks_default get_phi get_size_range_array get_time_elements getBiomass getCatchability getColours getCommunitySlope getComponent getCriticalFeedingLevel getDiet getEffort getEGrowth getEncounter getERepro getEReproAndGrowth getESpawning getExtEncounter getExtMort getFeedingLevel getFMort getFMortGear getGrowthCurves getInitialEffort getInteraction getLinetypes getM2 getM2Background getMaturityProportion getMaxIntakeRate getMeanMaxWeight getMeanWeight getMetabolicRate getMetadata getMort getN getParams getPhiPrey getPredKernel getPredMort getPredRate getProportionOfLargeFish getRateFunction getRates getRDD getRDI getReproductionLevel getReproductionProportion getResourceCapacity getResourceDynamics getResourceLevel getResourceMort getResourceRate getSearchVolume getSelectivity getSSB getTimes getYield getYieldGear getZ given_species_params given_species_params<-idxFinalT initial_effort initial_effort<-initialN initialN<-initialNOther initialNOther<-initialNResource initialNResource<-intake_max intake_max<-interaction_matrix interaction_matrix<-knife_edge l2w log_breaks lognormal_pred_kernel matchBiomasses matchGrowth matchNumbers matchYields maturity maturity<-melt metab metab<-mizerEGrowth mizerEncounter mizerERepro mizerEReproAndGrowth mizerFeedingLevel mizerFMort mizerFMortGear mizerMort MizerParams mizerPredMort mizerPredRate mizerRates mizerRDI mizerResourceMort MizerSim N newCommunityParams newMultispeciesParams newSingleSpeciesParams newTraitParams noRDD NOther NResource other_params other_params<-plot plotBiomass plotBiomassObservedVsModel plotDataFrame plotDiet plotFeedingLevel plotFMort plotGrowthCurves plotlyBiomass plotlyBiomassObservedVsModel plotlyFeedingLevel plotlyFMort plotlyGrowthCurves plotlyPredMort plotlySpectra plotlyYield plotlyYieldGear plotlyYieldObservedVsModel plotM2 plotPredMort plotSpectra plotYield plotYieldGear plotYieldObservedVsModel power_law_pred_kernel pred_kernel pred_kernel<-project project_simple projectToSteady readParams removeComponent removeSpecies renameSpecies repro_prop repro_prop<-resource_capacity resource_capacity<-resource_constant resource_dynamics resource_dynamics<-resource_level resource_level<-resource_logistic resource_params resource_params<-resource_rate resource_rate<-resource_semichemostat RickerRDD saveParams scaleModel search_vol search_vol<-selectivity selectivity<-set_community_model set_multispecies_model set_species_param_default set_trait_model setBevertonHolt setColours setComponent setExtEncounter setExtMort setFishing setInitialValues setInteraction setLinetypes setMaxIntakeRate setMetabolicRate setMetadata setParams setPredKernel setRateFunction setReproduction setResource setRmax setSearchVolume SheperdRDD sigmoid_length sigmoid_weight species_params species_params<-steady steadySingleSpecies summary truncated_lognormal_pred_kernel upgradeParams upgradeSim valid_gears_arg valid_species_arg validEffortVector validGearParams validParams validSpeciesParams w w_full w2l

Dependencies:askpass assertthat base64enc bslib cachem cli colorspace cpp11 crayon crosstalk curl data.table deSolve digest dplyr evaluate fansi farver fastmap fontawesome fs generics ggplot2 ggrepel glue gtable highr hms htmltools htmlwidgets httr isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle lubridate magrittr MASS Matrix memoise mgcv mime munsell nlme openssl pillar pkgconfig plotly plyr prettyunits progress promises purrr R6 rappdirs RColorBrewer Rcpp reshape2 rlang rmarkdown sass scales stringi stringr sys tibble tidyr tidyselect timechange tinytex utf8 vctrs viridisLite withr xfun yaml

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Getting started with mizer

Rendered frommizer.Rmdusingknitr::rmarkdownon Aug 28 2024.

Last update: 2024-03-08
Started: 2019-04-07

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
mizer: Multi-species size-based modelling in R	mizer-package mizer
Add new species	addSpecies
Calculate age at maturity	age_mat
Calculate age at maturity from von Bertalanffy growth parameters	age_mat_vB
Animation of the abundance spectra	animateSpectra
Beverton Holt function to calculate density-dependent reproduction rate	BevertonHoltRDD
Box predation kernel	box_pred_kernel
Calculate selectivity from gear parameters	calc_selectivity
Calibrate the model scale to match total observed biomass	calibrateBiomass
Calibrate the model scale to match total observed number	calibrateNumber
Calibrate the model scale to match total observed yield	calibrateYield
Compare two MizerParams objects and print out differences	compareParams
Complete species parameter data frame with default values	completeSpeciesParams
Helper function to keep other components constant	constant_other
Choose egg production to keep egg density constant	constantEggRDI
Give constant reproduction rate	constantRDD
Replace a mizer function with a custom version	customFunction
Set defaults for predation kernel parameters	default_pred_kernel_params
Default editions	defaults_edition
Check whether two objects are different	different
Measure distance between current and previous state in terms of RDI	distanceMaxRelRDI
Measure distance between current and previous state in terms of fish abundances	distanceSSLogN
Length based double-sigmoid selectivity function	double_sigmoid_length
Create empty MizerParams object of the right size	emptyParams
Size spectra at end of simulation	finalN finalNResource
Values of other ecosystem components at end of simulation	finalNOther
Gear parameters	gear_params gear_params<-
Get default value for f0	get_f0_default
Get default value for gamma	get_gamma_default
Calculate initial population abundances	get_initial_n
Get default value for 'ks'	get_ks_default
Get values from feeding kernel function	get_phi
Determine reproduction rate needed for initial egg abundance	get_required_reproduction
Get size range array	get_size_range_array
Get_time_elements	get_time_elements
Calculate the total biomass of each species within a size range at each time step.	getBiomass
Calculate the slope of the community abundance	getCommunitySlope
Get information about other ecosystem components	getComponent
Get critical feeding level	getCriticalFeedingLevel
Get diet of predator at size, resolved by prey species	getDiet
Fishing effort used in simulation	getEffort
Get energy rate available for growth	getEGrowth
Get encounter rate	getEncounter
Get energy rate available for reproduction	getERepro
Get energy rate available for reproduction and growth	getEReproAndGrowth
Alias for 'getERepro()'	getESpawning
Get feeding level	getFeedingLevel
Get the total fishing mortality rate from all fishing gears by time, species and size.	getFMort
Get the fishing mortality by time, gear, species and size	getFMortGear
Get growth curves giving weight as a function of age	getGrowthCurves
Alias for 'getPredMort()'	getM2
Alias for 'getResourceMort()'	getM2Background
Calculate the mean maximum weight of the community	getMeanMaxWeight
Calculate the mean weight of the community	getMeanWeight
Get total mortality rate	getMort
Calculate the number of individuals within a size range	getN
Extract the parameter object underlying a simulation	getParams
Get available energy	getPhiPrey
Get total predation mortality rate	getPredMort
Get predation rate	getPredRate
Calculate the proportion of large fish	getProportionOfLargeFish
Get all rates	getRates
Get density dependent reproduction rate	getRDD
Get density independent rate of egg production	getRDI
Get reproduction level	getReproductionLevel
Get predation mortality rate for resource	getResourceMort
Calculate the SSB of species	getSSB
Times for which simulation results are available	getTimes
Calculate the rate at which biomass of each species is fished	getYield
Calculate the rate at which biomass of each species is fished by each gear	getYieldGear
Alias for 'getMort()'	getZ
Time index at end of simulation	idxFinalT
Description of indicator functions	indicator_functions
Initial fishing effort	initial_effort initial_effort<- validEffortVector
Initial values for fish spectra	initialN initialN<-
Initial values for other ecosystem components	initialNOther initialNOther<-
Initial value for resource spectrum	initialNResource initialNResource<-
Alias for 'NS_interaction'	inter
Weight based knife-edge selectivity function	knife_edge
Length-weight conversion	l2w w2l
Lognormal predation kernel	lognormal_pred_kernel
Match biomasses to observations	matchBiomasses
Adjust model to produce observed growth	matchGrowth
Match numbers to observations	matchNumbers
Match yields to observations	matchYields
Get energy rate available for growth needed to project standard mizer model	mizerEGrowth
Get encounter rate needed to project standard mizer model	mizerEncounter
Get energy rate available for reproduction needed to project standard mizer model	mizerERepro
Get energy rate available for reproduction and growth needed to project standard mizer model	mizerEReproAndGrowth
Get feeding level needed to project standard mizer model	mizerFeedingLevel
Get the total fishing mortality rate from all fishing gears	mizerFMort
Get the fishing mortality needed to project standard mizer model	mizerFMortGear
Get total mortality rate needed to project standard mizer model	mizerMort
Alias for 'set_multispecies_model()'	MizerParams
A class to hold the parameters for a size based model.	MizerParams-class
Get total predation mortality rate needed to project standard mizer model	mizerPredMort
Get predation rate needed to project standard mizer model	mizerPredRate
Get all rates needed to project standard mizer model	mizerRates
Get density-independent rate of reproduction needed to project standard mizer model	mizerRDI
Get predation mortality rate for resource needed to project standard mizer model	mizerResourceMort
Constructor for the 'MizerSim' class	MizerSim
A class to hold the results of a simulation	MizerSim-class
Time series of size spectra	N NResource
Determine whether a MizerParams or MizerSim object needs to be upgraded	needs_upgrading
Set up parameters for a community-type model	newCommunityParams
Set up parameters for a general multispecies model	newMultispeciesParams
Set up parameters for a single species in a power-law background	newSingleSpeciesParams
Set up parameters for a trait-based multispecies model	newTraitParams
Give density-independent reproduction rate	noRDD
Time series of other components	NOther
Example interaction matrix for the North Sea example	NS_interaction
Example MizerParams object for the North Sea example	NS_params
Example MizerSim object for the North Sea example	NS_sim
Example species parameter set based on the North Sea	NS_species_params
Example species parameter set based on the North Sea with different gears	NS_species_params_gears
Summary plot for 'MizerSim' objects	plot,MizerParams,missing-method plot,MizerSim,missing-method
Plot the biomass of species through time	plotBiomass plotlyBiomass
Plotting observed vs. model biomass data	plotBiomassObservedVsModel plotlyBiomassObservedVsModel
Plot diet, resolved by prey species, as function of predator at size.	plotDiet
Plot the feeding level of species by size	plotFeedingLevel plotlyFeedingLevel
Plot total fishing mortality of each species by size	plotFMort plotlyFMort
Plot growth curves	plotGrowthCurves plotlyGrowthCurves
Alias for 'plotPredMort()'	plotM2
Plot predation mortality rate of each species against size	plotlyPredMort plotPredMort
Plot the abundance spectra	plotlySpectra plotSpectra
Description of the plotting functions	plotting_functions
Plot the total yield of species through time	plotlyYield plotYield
Plot the total yield of each species by gear through time	plotlyYieldGear plotYieldGear
Plotting observed vs. model yields	plotlyYieldObservedVsModel plotYieldObservedVsModel
Power-law predation kernel	power_law_pred_kernel
Project size spectrum forward in time	project
Project abundances by a given number of time steps into the future	project_simple
Project to steady state	projectToSteady
Remove species	removeSpecies
Rename species	renameSpecies
Keep resource abundance constant	resource_constant
Project resource using logistic model	balance_resource_logistic resource_logistic
Resource parameters	resource_params resource_params<-
Project resource using semichemostat model	balance_resource_semichemostat resource_semichemostat
Ricker function to calculate density-dependent reproduction rate	RickerRDD
Save a MizerParams object to file, and restore it	readParams saveParams
Change scale of the model	scaleModel
Deprecated function for setting up parameters for a community-type model	set_community_model
Deprecated obsolete function for setting up multispecies parameters	set_multispecies_model
Set a species parameter to a default value	set_species_param_default
Deprecated function for setting up parameters for a trait-based model	set_trait_model
Set Beverton-Holt reproduction without changing the steady state	setBevertonHolt
Set line colours and line types to be used in mizer plots	getColours getLinetypes setColours setLinetypes
Add a dynamical ecosystem component	removeComponent setComponent
Set external encounter rate	ext_encounter ext_encounter<- getExtEncounter setExtEncounter
Set external mortality rate	ext_mort ext_mort<- getExtMort setExtMort
Set fishing parameters	catchability catchability<- getCatchability getInitialEffort getSelectivity selectivity selectivity<- setFishing
Set initial values to values from a simulation	setInitialValues
Set species interaction matrix	interaction_matrix interaction_matrix<- setInteraction
Set maximum intake rate	getMaxIntakeRate intake_max intake_max<- setMaxIntakeRate
Set metabolic rate	getMetabolicRate metab metab<- setMetabolicRate
Set metadata for a model	getMetadata setMetadata
Set or change any model parameters	setParams
Set predation kernel	getPredKernel pred_kernel pred_kernel<- setPredKernel
Set own rate function to replace mizer rate function	getRateFunction other_params other_params<- setRateFunction
Set reproduction parameters	getMaturityProportion getReproductionProportion maturity maturity<- repro_prop repro_prop<- setReproduction
Set resource dynamics	resource_capacity resource_capacity<- resource_dynamics resource_dynamics<- resource_level resource_level<- resource_rate resource_rate<- setResource
Alias for 'setBevertonHolt()'	setRmax
Set search volume	getSearchVolume search_vol search_vol<- setSearchVolume
Sheperd function to calculate density-dependent reproduction rate	SheperdRDD
Length based sigmoid selectivity function	sigmoid_length
Weight based sigmoidal selectivity function	sigmoid_weight
Species parameters	calculated_species_params given_species_params given_species_params<- species_params species_params<-
Set initial values to a steady state for the model	steady
Set initial abundances to single-species steady state abundances	steadySingleSpecies
Description of summary functions	summary_functions
Summarize MizerParams object	summary,MizerParams-method
Summarize MizerSim object	summary,MizerSim-method
Truncated lognormal predation kernel	truncated_lognormal_pred_kernel
Upgrade MizerParams object from earlier mizer versions	upgradeParams
Upgrade MizerSim object from earlier mizer versions	upgradeSim
Helper function to assure validity of gears argument	valid_gears_arg
Helper function to assure validity of species argument	valid_species_arg
Check validity of gear parameters and set defaults	validGearParams
Validate MizerParams object and upgrade if necessary using 'upgradeParams()'.	validParams
Validate species parameter data frame	validSpeciesParams
Size bins	dw dw_full w w_full