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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.

Installation

You can install the released version of SAMtool from CRAN with:

install.packages("SAMtool")

And the development version from GitHub with:

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

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Version

Install

install.packages('SAMtool')

Monthly Downloads

782

Version

1.7.0

License

GPL-3

Issues

Pull Requests

Stars

Forks

Maintainer

Quang Huynh

Last Published

August 29th, 2024

Functions in SAMtool (1.7.0)

HCR_MSY

Harvest control rule to fish at some fraction of maximum sustainable yield
HCR_ramp

Linearly ramped harvest control rules
Model-based-MP

Model-based management procedures
Assessment-class

Class-Assessment
HCR_segment

Segmented harvest control rules
check_RCMdata

Rapid Conditioning Model (RCM)
SCA

Statistical catch-at-age (SCA) model
RCM2MOM

Convert RCM to a multi-fleet operating model (MOM)
RCM_assess

The rapid conditioning model as an assessment function
SCA_CAL

Age-structured model using fishery length composition
RCModel-class

Class-RCModel
SAMtool-package

Stock Assessment Methods Toolkit
RCMdata-class

Class-RCMdata
DD_TMB

Delay - Difference Stock Assessment in TMB
PRBcalc

Calculate mahalanobis distance (null and alternative MSEs) and statistical power for all MPs in an MSE
SP

Surplus production model with FMSY and MSY as leading parameters
SSS

Simple Stock Synthesis
Probs

Calculates mahalanobis distance and rejection of the Null operating model
SP_production

Find the production parameter based on depletion that produces MSY
Shortcut

Assessment emulator as a shortcut to model fitting in closed-loop simulation
SCA_DDM

SCA models with time-varying natural mortality
cDD

Continuous Delay-differential assessment model
TAC_MSY

Calculate MSY-based TAC from Assessment object
pcod

Pacific cod in Area 5ABCD (Hecate Strait and Queen Charlotte Sound), British Columbia, Canada
plot_timeseries

Plot time series of data
VPA

Virtual population analysis (VPA)
mahplot

Plot statistical power of the indicator with increasing time blocks
make_interim_MP

Make a custom management procedure (MP)
profile,Assessment-method

Profile likelihood of assessment models
posterior

Sample posterior of TMB models in SAMtool
plot.RCModel

Plot RCM scope output
prelim_AM

Preliminary Assessments in MSE
SCA_RWM

SCA with random walk in M
compare_models

Compare output from several assessment models
plot.retro

Methods for retro object
prof-class

Class-prof
plot.prof

Plot profile object
plot.Assessment

Plot Assessment object
summary.Assessment

Summary of Assessment object
plot_crosscorr

Produce a cross-correlation plot of the derived data arising from getinds(MSE_object)
diagnostic

Diagnostic of assessments in MSE: did Assess models converge during MSE?
plot_SR

Plot stock-recruitment function
plot_lognormalvar

Plots a lognormal variable
plot_betavar

Plots a beta variable
swordfish

North Atlantic Swordfish dataset
plot_steepness

Plots probability distribution function of stock-recruit steepness
project-class

Class-project
plot_residuals

Plot residuals
plot_composition

Plot composition data
retrospective

Retrospective analysis of assessment models
getinds

Characterize posterior predictive data
projection

Projections for assessment models
retro-class

Class-retro
sim-class

Class-sim
retrospective_AM

retrospective_AM (retrospective of Assessment model in MSE)
userguide

Get the SAMtool vignettes
simulate

Generate simulated data from TMB models in SAMtool
HCR_FB

A Harvest Control Rule using B/BMSY and F/FMSY to adjust TAC or TAE.
HCR_escapement

Fixed escapement harvest control rule
HCR_fixedF

Simple fixed F harvest control rule
HCRlin

Generic linear harvest control rule based on biomass