Class

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.
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]. The broodtake of natural origin spawners.
HOB: Array [nsim, nstocks, proyears]. The broodtake of hatchery origin spawners.
NOS: Array [nsim, nstocks, proyears]. Natural origin spawners.
HOS: Array [nsim, nstocks, proyears]. Hatchery origin spawners.
HOS_effective: Array [nsim, nstocks, proyears]. Hatchery origin spawners 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, proyears]. Pre-terminal fishery harvest rate (from kept catch) of natural origin spawners.
UT_NOS: Array [nsim, nstocks, proyears]. Terminal fishery harvest rate of natural origin spawners.
UPT_HOS: Array [nsim, nstocks, proyears]. Pre-terminal fishery harvest rate of hatchery origin spawners.
UT_HOS: Array [nsim, nstocks, proyears]. Terminal fishery harvest rate of hatchery origin spawners.
ExPT_NOS: Array [nsim, nstocks, proyears]. Pre-terminal fishery exploitation rate (from kept catch and dead releases) of natural origin spawners.
ExT_NOS: Array [nsim, nstocks, proyears]. Terminal fishery exploitation rate of natural origin spawners.
ExPT_HOS: Array [nsim, nstocks, proyears]. Pre-terminal fishery exploitation rate of hatchery origin spawners.
ExT_HOS: Array [nsim, nstocks, 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. Contains Ref for reference points, SHist for the SHist object, and SOM for the SOM object.

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:       Smolt_NOS      Smolt_HOS      Smolt_Rel       Njuv_NOS
#> Class:          array          array          array          array
#>                                                                   
#> Name:        Njuv_HOS     Return_NOS     Return_HOS Escapement_NOS
#> Class:          array          array          array          array
#>                                                                   
#> Name:  Escapement_HOS            NOB            HOB            NOS
#> Class:          array          array          array          array
#>                                                                   
#> Name:             HOS  HOS_effective        KPT_NOS         KT_NOS
#> Class:          array          array          array          array
#>                                                                   
#> Name:         KPT_HOS         KT_HOS        DPT_NOS         DT_NOS
#> Class:          array          array          array          array
#>                                                                   
#> Name:         DPT_HOS         DT_HOS        UPT_NOS         UT_NOS
#> Class:          array          array          array          array
#>                                                                   
#> Name:         UPT_HOS         UT_HOS       ExPT_NOS        ExT_NOS
#> Class:          array          array          array          array
#>                                                                   
#> Name:        ExPT_HOS        ExT_HOS        fitness           pNOB
#> Class:          array          array          array          array
#>                                                                   
#> Name:     pHOS_census pHOS_effective      Mjuv_loss            PNI
#> Class:          array          array          array          array
#>                                     
#> Name:          p_wild           Misc
#> Class:          array           list