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Class "SMSE"

Source: R/define-SOM.R
SMSE-class.Rd

Stores the outputs from the simulation of salmon operating models.

Details

In generation \(t\), proportionate natural influence (PNI) is defined as:

$$\textrm{PNI}_t = \dfrac{p^\textrm{NOB}_t}{p^\textrm{NOB}_t + p^\textrm{HOSeff}_t}$$

with \(p^\textrm{HOSeff} = \textrm{HOSeff}/(\textrm{NOS} + \textrm{HOSeff})\).

The proportion of wild salmon is defined as:

$$p^{\textrm{WILD}}_t = q^\textrm{HOScen}_t \dfrac{(q^\textrm{HOScen}_{t-1})^2} {(q^\textrm{HOScen}_{t-1})^2 + 2\gamma \times p^\textrm{HOScen}_{t-1} q^\textrm{HOScen}_{t-1} + \gamma^2 (p^\textrm{HOScen}_{t-1})^2}$$

where \(q = 1-p\) and \(p^\textrm{HOScen} = \textrm{HOS}/(\textrm{NOS} + \textrm{HOS})\).

Slots

Name

Character. Identifying name

nyears

Integer. The number of historical years

proyears

Integer. The number of projected years

nsim

Integer. The number of simulations

nstocks

Integer. The number of stocks

Snames

Character. Stock names

Egg_NOS

Array [nsim, nstocks, proyears]. Spawning output, i.e., egg production, of natural origin spawners.

Egg_HOS

Array [nsim, nstocks, proyears]. Spawning output of hatchery origin spawners.

Fry_NOS

Array [nsim, nstocks, proyears]. Fry that are offspring of natural origin spawners.

Fry_HOS

Array [nsim, nstocks, proyears]. Fry that are offspring of hatchery origin spawners.

Smolt_NOS

Array [nsim, nstocks, proyears]. Smolts that are offspring of natural origin spawners.

Smolt_HOS

Array [nsim, nstocks, proyears]. Smolts that are offspring of hatchery origin spawners.

Smolt_Rel

Array [nsim, nstocks, proyears]. Smolts that are offspring of broodtake, i.e., hatchery releases.

Njuv_NOS

Array [nsim, nstocks, nage, proyears]. Abundance of juvenile natural origin fish at the beginning of the year.

Njuv_HOS

Array [nsim, nstocks, nage, proyears]. Abundance of juvenile hatchery origin fish at the beginning of the year.

Return_NOS

Array [nsim, nstocks, nage, proyears]. Mature fish that will be natural origin spawners.

Return_HOS

Array [nsim, nstocks, nage, proyears]. Mature fish that will be hatchery origin spawners.

Escapement_NOS

Array [nsim, nstocks, nage, proyears]. The escapement of mature fish that will be natural origin spawners.

Escapement_HOS

Array [nsim, nstocks, nage, proyears]. The escapement of mature fish that will be hatchery origin spawners.

NOB

Array [nsim, nstocks, proyears]. Natural origin broodtake.

HOB

Array [nsim, nstocks, proyears]. Hatchery origin broodtake (local + strays).

HOB_stray

Array [nsim, nstocks, proyears]. Hatchery origin broodtake (strays only).

HOB_import

Array [nsim, nstocks, proyears]. Imported hatchery origin broodtake used for hatchery production.

NOS

Array [nsim, nstocks, nage, proyears]. Natural origin spawners.

HOS

Array [nsim, nstocks, nage, proyears]. Hatchery origin spawners (local + strays).

HOS_stray

Array [nsim, nstocks, nage, proyears]. Hatchery origin spawners (strays only).

HOS_effective

Array [nsim, nstocks, nage, proyears]. Hatchery origin spawners (local + strays) discounted by gamma.

KPT_NOS

Array [nsim, nstocks, proyears]. Pre-terminal fishery kept catch of natural origin spawners.

KT_NOS

Array [nsim, nstocks, proyears]. Terminal fishery kept catch of natural origin spawners.

KPT_HOS

Array [nsim, nstocks, proyears]. Pre-terminal fishery kept catch of hatchery origin spawners.

KT_HOS

Array [nsim, nstocks, proyears]. Terminal fishery kept catch of hatchery origin spawners.

DPT_NOS

Array [nsim, nstocks, proyears]. Pre-terminal fishery released catch (live and dead) of natural origin spawners.

DT_NOS

Array [nsim, nstocks, proyears]. Terminal fishery released catch (live and dead) of natural origin spawners.

DPT_HOS

Array [nsim, nstocks, proyears]. Pre-terminal fishery released catch (live and dead) of hatchery origin spawners.

DT_HOS

Array [nsim, nstocks, proyears]. Terminal fishery released catch (live and dead) hatchery origin spawners.

UPT_NOS

Array [nsim, nstocks, nage, proyears]. Pre-terminal fishery harvest rate (from kept catch) of natural origin spawners.

UT_NOS

Array [nsim, nstocks, nage, proyears]. Terminal fishery harvest rate of natural origin spawners.

UPT_HOS

Array [nsim, nstocks, nage, proyears]. Pre-terminal fishery harvest rate of hatchery origin spawners.

UT_HOS

Array [nsim, nstocks, nage, proyears]. Terminal fishery harvest rate of hatchery origin spawners.

ExPT_NOS

Array [nsim, nstocks, nage, proyears]. Pre-terminal fishery exploitation rate (from kept catch and dead releases) of natural origin spawners.

ExT_NOS

Array [nsim, nstocks, nage, proyears]. Terminal fishery exploitation rate of natural origin spawners.

ExPT_HOS

Array [nsim, nstocks, nage, proyears]. Pre-terminal fishery exploitation rate of hatchery origin spawners.

ExT_HOS

Array [nsim, nstocks, nage, proyears]. Terminal fishery exploitation rate of hatchery origin spawners.

fitness

Array [nsim, nstocks, 2, proyears]. Fitness of the population in the natural (1) and hatchery (2) environments.

pNOB

Array [nsim, nstocks, proyears]. Proportion of natural fish in the brood.

pHOS_census

Array [nsim, nstocks, proyears]. Proportion of spawners of hatchery origin, weighted by age class fecundity.

pHOS_effective

Array [nsim, nstocks, proyears]. Proportion of spawners of hatchery origin, discounted by gamma, weighted by age class fecundity.

PNI

Array [nsim, nstocks, proyears]. Proportionate natural influence, index of gene flow from hatchery to the natural environment.

p_wild

Array [nsim, nstocks, proyears]. Proportion of wild spawners, natural spawners whose parents were also produced in the natural environment assuming non-assortative mating, defined under Canada's Wild Salmon Policy.

Mjuv_loss

Array [nsim, nstocks, nage, proyears]. Realized juvenile natural mortality, which may differ from inputs due to fitness loss.

Misc

List. Miscellaneous output:

  • Ref for reference points

  • SHist for the SHist object

  • SOM for the SOM object.

  • LHG list nstocks long containing state variables by life history group

Creating Object

Objects can be created by calls of the form new("SMSE")

References

Withler et al. 2018. Genetically Based Targets for Enhanced Contributions to Canadian Pacific Chinook Salmon Populations. DFO Can. Sci. Advis. Sec. Res. Doc. 2018/019. xii + 88 p.

Examples

showClass("SMSE")
#> Class "SMSE" [package "salmonMSE"]
#> 
#> Slots:
#>                                                                   
#> Name:            Name         nyears       proyears           nsim
#> Class:      character        numeric        numeric        numeric
#>                                                                   
#> Name:         nstocks         Snames        Egg_NOS        Egg_HOS
#> Class:        numeric      character          array          array
#>                                                                   
#> Name:         Fry_NOS        Fry_HOS      Smolt_NOS      Smolt_HOS
#> Class:          array          array          array          array
#>                                                                   
#> Name:       Smolt_Rel       Njuv_NOS       Njuv_HOS     Return_NOS
#> Class:          array          array          array          array
#>                                                                   
#> Name:      Return_HOS Escapement_NOS Escapement_HOS            NOB
#> Class:          array          array          array          array
#>                                                                   
#> Name:             HOB      HOB_stray     HOB_import            NOS
#> Class:          array          array          array          array
#>                                                                   
#> Name:             HOS      HOS_stray  HOS_effective        KPT_NOS
#> Class:          array          array          array          array
#>                                                                   
#> Name:          KT_NOS        KPT_HOS         KT_HOS        DPT_NOS
#> Class:          array          array          array          array
#>                                                                   
#> Name:          DT_NOS        DPT_HOS         DT_HOS        UPT_NOS
#> Class:          array          array          array          array
#>                                                                   
#> Name:          UT_NOS        UPT_HOS         UT_HOS       ExPT_NOS
#> Class:          array          array          array          array
#>                                                                   
#> Name:         ExT_NOS       ExPT_HOS        ExT_HOS        fitness
#> Class:          array          array          array          array
#>                                                                   
#> Name:            pNOB    pHOS_census pHOS_effective      Mjuv_loss
#> Class:          array          array          array          array
#>                                                    
#> Name:             PNI         p_wild           Misc
#> Class:          array          array           list