# salmonMSE

> Management Strategy Evaluation for Salmon Species

salmonMSE is a decision-support tool for Pacific salmon focusing on
strategic trade-offs among harvest, hatchery and habitat management
levers.

Funding for the development of salmonMSE is provided through the
[Pacific Salmon Strategy
Initiative](https://www.dfo-mpo.gc.ca/campaign-campagne/pss-ssp/index-eng.html)
in collaboration with the Department of Fisheries and Oceans Canada.

## Installation

salmonMSE can be downloaded from [CRAN](https://CRAN.R-project.org)
with:

``` r

install.packages("salmonMSE")
```

And the development version is available on
[GitHub](https://github.com/) with:

``` r

# install.packages("remotes")
remotes::install_github("Blue-Matter/salmonMSE")
```

# Package index

## All functions

- [`AHA()`](https://docs.salmonmse.com/reference/AHA.md) : All-H
  Analyzer

- [`Bio-class`](https://docs.salmonmse.com/reference/Bio-class.md) :

  Class `"Bio"`

- [`CM2SOM()`](https://docs.salmonmse.com/reference/CM2SOM.md) : Convert
  conditioning model to operating model

- [`CM_MSY()`](https://docs.salmonmse.com/reference/CM_MSY.md)
  [`CM_Sgen()`](https://docs.salmonmse.com/reference/CM_MSY.md) : Plot
  reference points from conditioning model

- [`get_report()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`get_CMdata()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`CM_trace()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`CM_pairs()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`CM_fit_esc()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`CM_fit_pHOS()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`CM_fit_CWTesc()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`CM_fit_CWTcatch()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`CM_maturity()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`CM_vul()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`CM_SRR()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`CM_prod()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`CM_Srep()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`CM_M()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`CM_Megg()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`CM_Njuv()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`CM_recr()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`CM_esc()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`CM_F()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`CM_surv()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`CM_wt()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`CM_surv2()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`CM_wto()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`CM_ER()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`CM_CWT_ER()`](https://docs.salmonmse.com/reference/CMfigures.md)
  [`CM_covariate()`](https://docs.salmonmse.com/reference/CMfigures.md)
  : Figures for conditioning model results

- [`Habitat-class`](https://docs.salmonmse.com/reference/Habitat-class.md)
  :

  Class `"Habitat"`

- [`Harvest-class`](https://docs.salmonmse.com/reference/Harvest-class.md)
  :

  Class `"Harvest"`

- [`Hatchery-class`](https://docs.salmonmse.com/reference/Hatchery-class.md)
  :

  Class `"Hatchery"`

- [`Historical-class`](https://docs.salmonmse.com/reference/Historical-class.md)
  :

  Class `"Historical"`

- [`PNI50()`](https://docs.salmonmse.com/reference/PNI50.md)
  [`PNI80()`](https://docs.salmonmse.com/reference/PNI50.md)
  [`WILD50()`](https://docs.salmonmse.com/reference/PNI50.md)
  [`SMSY85()`](https://docs.salmonmse.com/reference/PNI50.md)
  [`Sgen100()`](https://docs.salmonmse.com/reference/PNI50.md) : Example
  performance metrics

- [`SMSE-class`](https://docs.salmonmse.com/reference/SMSE-class.md) :

  Class `"SMSE"`

- [`SOM-class`](https://docs.salmonmse.com/reference/SOM-class.md)
  [`SOM`](https://docs.salmonmse.com/reference/SOM-class.md) :

  Class `"SOM"`

- [`calc_SRR()`](https://docs.salmonmse.com/reference/calc_SRR.md) :
  Calculate abundance from density-dependent mortality

- [`calc_SRRpars()`](https://docs.salmonmse.com/reference/calc_SRRpars.md)
  : Convert density-dependent survival parameters

- [`calc_Smsy_Ricker()`](https://docs.salmonmse.com/reference/calc_Smsy_Ricker.md)
  [`calc_Umsy_Ricker()`](https://docs.salmonmse.com/reference/calc_Smsy_Ricker.md)
  [`calc_Sgen_Ricker()`](https://docs.salmonmse.com/reference/calc_Smsy_Ricker.md)
  : Ricker reference points

- [`calc_ref()`](https://docs.salmonmse.com/reference/calc_ref.md)
  [`calc_MSY()`](https://docs.salmonmse.com/reference/calc_ref.md)
  [`calc_Sgen()`](https://docs.salmonmse.com/reference/calc_ref.md) :
  Reference points

- [`calc_smolt()`](https://docs.salmonmse.com/reference/calc_smolt.md) :
  Smolt production

- [`check_SOM()`](https://docs.salmonmse.com/reference/check_SOM.md) :
  Check inputs to SOM object

- [`compare()`](https://docs.salmonmse.com/reference/compare.md) :
  Compare scenarios in markdown

- [`compare_spawners()`](https://docs.salmonmse.com/reference/compare_spawners.md)
  [`compare_fitness()`](https://docs.salmonmse.com/reference/compare_spawners.md)
  [`compare_escapement()`](https://docs.salmonmse.com/reference/compare_spawners.md)
  : Compare simulation runs

- [`compare_statevar_ts()`](https://docs.salmonmse.com/reference/compare_statevar_ts.md)
  [`compare_statevar_hist()`](https://docs.salmonmse.com/reference/compare_statevar_ts.md)
  : Compare state variables from simulation runs

- [`fit_CM()`](https://docs.salmonmse.com/reference/fit_CM.md)
  [`sample_CM()`](https://docs.salmonmse.com/reference/fit_CM.md) : Fit
  conditioning model to historical data

- [`glossary`](https://docs.salmonmse.com/reference/glossary.md) :
  salmonMSE glossary

- [`plot_LHG()`](https://docs.salmonmse.com/reference/plot_LHG.md)
  [`plot_RS()`](https://docs.salmonmse.com/reference/plot_LHG.md) : Plot
  life history groups and release strategies

- [`plot_decision_table()`](https://docs.salmonmse.com/reference/plot_decision_table.md)
  [`plot_decision_table2()`](https://docs.salmonmse.com/reference/plot_decision_table.md)
  : Decision table of performance metrics

- [`plot_statevar_ts()`](https://docs.salmonmse.com/reference/plot_statevar_ts.md)
  [`plot_statevar_hist()`](https://docs.salmonmse.com/reference/plot_statevar_ts.md)
  [`plot_spawners()`](https://docs.salmonmse.com/reference/plot_statevar_ts.md)
  [`plot_fitness()`](https://docs.salmonmse.com/reference/plot_statevar_ts.md)
  [`plot_escapement()`](https://docs.salmonmse.com/reference/plot_statevar_ts.md)
  [`plot_fishery()`](https://docs.salmonmse.com/reference/plot_statevar_ts.md)
  [`plot_Kobe()`](https://docs.salmonmse.com/reference/plot_statevar_ts.md)
  : Plot core output from salmonMSE

- [`plot_tradeoff()`](https://docs.salmonmse.com/reference/plot_tradeoff.md)
  : Tradeoff figure

- [`report(`*`<SMSE>`*`)`](https://docs.salmonmse.com/reference/report.md)
  : Generate markdown reports

- [`report_CM()`](https://docs.salmonmse.com/reference/report_CM.md) :
  Conditioning model markdown report

- [`salmonMSE()`](https://docs.salmonmse.com/reference/salmonMSE.md)
  [`ProjectSOM()`](https://docs.salmonmse.com/reference/salmonMSE.md) :
  Run salmonMSE

- [`salmonMSE_env`](https://docs.salmonmse.com/reference/salmonMSE_env.md)
  : Environment to store salmon specific variables, e.g, fitness, during
  the simulation

- [`simple_SOM`](https://docs.salmonmse.com/reference/simple_SOM.md)
  [`multi_SOM`](https://docs.salmonmse.com/reference/simple_SOM.md) :
  Example objects from salmonMSE

# Articles

### All vignettes

- [Conditioning model from CWT and
  escapement](https://docs.salmonmse.com/articles/conditioning.md):
- [Decision
  table](https://docs.salmonmse.com/articles/decision-table.md):
- [Dynamics
  equations](https://docs.salmonmse.com/articles/equations.md):
- [Multi-population
  model](https://docs.salmonmse.com/articles/example-multi.md):
- [Simple salmonMSE
  example](https://docs.salmonmse.com/articles/example.md):
- [Introduction](https://docs.salmonmse.com/articles/introduction.md):
- [Reference points](https://docs.salmonmse.com/articles/ref.md):