# SAMtool

The Stock Assessment Methods toolkit (`SAMtool`) is a collection of
assessment methods and management procedures that have been developed
for more data-intensive applications. This package includes the Rapid
Conditioning Model for conditioning operating models in data-moderate
and data-rich fisheries.

SAMtool is part of the `openMSE` collection of packages.

You can learn more about the `openMSE` packages at the [openMSE
documentation site](https://openMSE.com).

## Installation

You can install the released version of SAMtool from
[CRAN](https://CRAN.R-project.org) with:

``` r

install.packages("SAMtool")
```

And the development version from
[GitHub](https://github.com/Blue-Matter/SAMtool) with:

``` r

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

# Package index

## Rapid Conditioning Model

A population model intended for conditioning operating models from
data-sparse to data-rich applications.

- [`check_RCMdata()`](https://samtool.openmse.com/reference/RCM.md)
  [`RCM()`](https://samtool.openmse.com/reference/RCM.md) : Rapid
  Conditioning Model (RCM)
- [`RCM2MOM()`](https://samtool.openmse.com/reference/RCM2MOM.md) :
  Convert RCM to a multi-fleet operating model (MOM)

## Management procedures

Make a management procedure from an assessment and control rule or use a
suite of pre-made MPs.

- [`make_interim_MP()`](https://samtool.openmse.com/reference/make_MP.md)
  [`make_projection_MP()`](https://samtool.openmse.com/reference/make_MP.md)
  [`make_MP()`](https://samtool.openmse.com/reference/make_MP.md) : Make
  a custom management procedure (MP)
- [`SCA_MSY()`](https://samtool.openmse.com/reference/Model-based-MP.md)
  [`SCA_75MSY()`](https://samtool.openmse.com/reference/Model-based-MP.md)
  [`SCA_4010()`](https://samtool.openmse.com/reference/Model-based-MP.md)
  [`DDSS_MSY()`](https://samtool.openmse.com/reference/Model-based-MP.md)
  [`DDSS_75MSY()`](https://samtool.openmse.com/reference/Model-based-MP.md)
  [`DDSS_4010()`](https://samtool.openmse.com/reference/Model-based-MP.md)
  [`SP_MSY()`](https://samtool.openmse.com/reference/Model-based-MP.md)
  [`SP_75MSY()`](https://samtool.openmse.com/reference/Model-based-MP.md)
  [`SP_4010()`](https://samtool.openmse.com/reference/Model-based-MP.md)
  [`SSS_MSY()`](https://samtool.openmse.com/reference/Model-based-MP.md)
  [`SSS_75MSY()`](https://samtool.openmse.com/reference/Model-based-MP.md)
  [`SSS_4010()`](https://samtool.openmse.com/reference/Model-based-MP.md)
  : Model-based management procedures

## Population models

Assessment models that can be fitted with a Data object for closed-loop
simulation.

- [`cDD()`](https://samtool.openmse.com/reference/cDD.md)
  [`cDD_SS()`](https://samtool.openmse.com/reference/cDD.md) :
  Continuous Delay-differential assessment model
- [`DD_TMB()`](https://samtool.openmse.com/reference/DD_TMB.md)
  [`DD_SS()`](https://samtool.openmse.com/reference/DD_TMB.md) : Delay -
  Difference Stock Assessment in TMB
- [`SCA()`](https://samtool.openmse.com/reference/SCA.md)
  [`SCA2()`](https://samtool.openmse.com/reference/SCA.md)
  [`SCA_Pope()`](https://samtool.openmse.com/reference/SCA.md) :
  Statistical catch-at-age (SCA) model
- [`SCA_CAL()`](https://samtool.openmse.com/reference/SCA_CAL.md) :
  Age-structured model using fishery length composition
- [`SCA_DDM()`](https://samtool.openmse.com/reference/SCA_DDM.md) : SCA
  models with time-varying natural mortality
- [`SCA_RWM()`](https://samtool.openmse.com/reference/SCA_RWM.md) : SCA
  with random walk in M
- [`SP()`](https://samtool.openmse.com/reference/SP.md)
  [`SP_SS()`](https://samtool.openmse.com/reference/SP.md)
  [`SP_Fox()`](https://samtool.openmse.com/reference/SP.md) : Surplus
  production model with FMSY and MSY as leading parameters
- [`RCM_assess()`](https://samtool.openmse.com/reference/RCM_assess.md)
  : The rapid conditioning model as an assessment function
- [`SSS()`](https://samtool.openmse.com/reference/SSS.md) : Simple Stock
  Synthesis
- [`Shortcut()`](https://samtool.openmse.com/reference/Shortcut.md)
  [`Shortcut2()`](https://samtool.openmse.com/reference/Shortcut.md)
  [`Perfect()`](https://samtool.openmse.com/reference/Shortcut.md) :
  Assessment emulator as a shortcut to model fitting in closed-loop
  simulation
- [`VPA()`](https://samtool.openmse.com/reference/VPA.md) : Virtual
  population analysis (VPA)
- [`projection()`](https://samtool.openmse.com/reference/projection.md)
  : Projections for assessment models

## Harvest control rules

Functions to pair with an assessment model to create a catch-based
managment procedure.

- [`HCR_MSY()`](https://samtool.openmse.com/reference/HCR_MSY.md) :
  Harvest control rule to fish at some fraction of maximum sustainable
  yield
- [`HCR_escapement()`](https://samtool.openmse.com/reference/HCR_escapement.md)
  : Fixed escapement harvest control rule
- [`HCR_fixedF()`](https://samtool.openmse.com/reference/HCR_fixedF.md)
  : Simple fixed F harvest control rule
- [`HCR_segment()`](https://samtool.openmse.com/reference/HCR_segment.md)
  : Segmented harvest control rules
- [`HCR_ramp()`](https://samtool.openmse.com/reference/HCR_ramp.md)
  [`HCR40_10()`](https://samtool.openmse.com/reference/HCR_ramp.md)
  [`HCR60_20()`](https://samtool.openmse.com/reference/HCR_ramp.md)
  [`HCR80_40MSY()`](https://samtool.openmse.com/reference/HCR_ramp.md) :
  Linearly ramped harvest control rules

## Utility functions

Functions to evaluate behavior of assessment models.

- [`compare_models()`](https://samtool.openmse.com/reference/compare_models.md)
  : Compare output from several assessment models
- [`diagnostic()`](https://samtool.openmse.com/reference/diagnostic.md)
  [`diagnostic_AM()`](https://samtool.openmse.com/reference/diagnostic.md)
  : Diagnostic of assessments in MSE: did Assess models converge during
  MSE?
- [`posterior()`](https://samtool.openmse.com/reference/posterior.md)
  [`RCMstan()`](https://samtool.openmse.com/reference/posterior.md) :
  Sample posterior of TMB models in SAMtool
- [`prelim_AM()`](https://samtool.openmse.com/reference/prelim_AM.md) :
  Preliminary Assessments in MSE
- [`profile(`*`<Assessment>`*`)`](https://samtool.openmse.com/reference/profile.md)
  [`profile(`*`<RCModel>`*`)`](https://samtool.openmse.com/reference/profile.md)
  : Profile likelihood of assessment models
- [`simulate(`*`<Assessment>`*`)`](https://samtool.openmse.com/reference/simulate.md)
  [`simulate(`*`<RCModel>`*`)`](https://samtool.openmse.com/reference/simulate.md)
  : Generate simulated data from TMB models in SAMtool
- [`retrospective()`](https://samtool.openmse.com/reference/retrospective.md)
  : Retrospective analysis of assessment models
- [`retrospective_AM()`](https://samtool.openmse.com/reference/retrospective_AM.md)
  : retrospective_AM (retrospective of Assessment model in MSE)

## Plotting functions

Generate summary and figures of assessment output.

- [`summary(`*`<Assessment>`*`)`](https://samtool.openmse.com/reference/summary.Assessment.md)
  : Summary of Assessment object
- [`plot(`*`<RCModel>`*`,`*`<missing>`*`)`](https://samtool.openmse.com/reference/plot.RCModel.md)
  [`compare_RCM()`](https://samtool.openmse.com/reference/plot.RCModel.md)
  : Plot RCM scope output
- [`plot(`*`<Assessment>`*`,`*`<missing>`*`)`](https://samtool.openmse.com/reference/plot.Assessment.md)
  [`plot(`*`<Assessment>`*`,`*`<retro>`*`)`](https://samtool.openmse.com/reference/plot.Assessment.md)
  : Plot Assessment object
- [`plot(`*`<prof>`*`,`*`<missing>`*`)`](https://samtool.openmse.com/reference/plot.prof.md)
  : Plot profile object
- [`plot(`*`<retro>`*`,`*`<missing>`*`)`](https://samtool.openmse.com/reference/plot.retro.md)
  [`summary(`*`<retro>`*`)`](https://samtool.openmse.com/reference/plot.retro.md)
  : Methods for retro object
- [`plot_SR()`](https://samtool.openmse.com/reference/plot_SR.md) : Plot
  stock-recruitment function
- [`plot_betavar()`](https://samtool.openmse.com/reference/plot_betavar.md)
  : Plots a beta variable
- [`plot_composition()`](https://samtool.openmse.com/reference/plot_composition.md)
  : Plot composition data
- [`plot_lognormalvar()`](https://samtool.openmse.com/reference/plot_lognormalvar.md)
  : Plots a lognormal variable
- [`plot_residuals()`](https://samtool.openmse.com/reference/plot_residuals.md)
  : Plot residuals
- [`plot_steepness()`](https://samtool.openmse.com/reference/plot_steepness.md)
  : Plots probability distribution function of stock-recruit steepness
- [`plot_timeseries()`](https://samtool.openmse.com/reference/plot_timeseries.md)
  : Plot time series of data

## Data indicators

Calculate the statistical power of data indicators, generated in
closed-loop simulation, to detect differences between operating models
([Carruthers and Hordyk 2018](https://doi.org/10.1139/cjfas-2018-0223)).

- [`PRBcalc()`](https://samtool.openmse.com/reference/PRBcalc.md) :
  Calculate mahalanobis distance (null and alternative MSEs) and
  statistical power for all MPs in an MSE
- [`Probs()`](https://samtool.openmse.com/reference/Probs.md) :
  Calculates mahalanobis distance and rejection of the Null operating
  model
- [`getinds()`](https://samtool.openmse.com/reference/getinds.md) :
  Characterize posterior predictive data
- [`mahplot()`](https://samtool.openmse.com/reference/mahplot.md) : Plot
  statistical power of the indicator with increasing time blocks
- [`plot_crosscorr()`](https://samtool.openmse.com/reference/plot_crosscorr.md)
  : Produce a cross-correlation plot of the derived data arising from
  getinds(MSE_object)