Package: FLSAM 3.0.0.9005

N.T. Hintzen

FLSAM: An Implementation of the State-Space Assessment Model for FLR

This package provides an FLR wrapper to the SAM state-space assessment model.

Authors:N.T. Hintzen [cre], M.R. Payne [aut]

# Install 'FLSAM' in R:

install.packages('FLSAM', repos = c('https://flr.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

On CRAN:

Last updated from:89bb528f43. Checks:4 ERROR, 2 OK, 3 WARNING. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	ERROR	180
source / vignettes	OK	177
linux-release-x86_64	WARNING	341
macos-release-arm64	ERROR	128
macos-oldrel-arm64	ERROR	134
windows-devel	ERROR	139
windows-release	WARNING	468
windows-oldrel	WARNING	429
wasm-release	OK	101

Help page	Topics
Accessor functions for FLSAM	accessors catch catchabilities f fbar n obs.var power.law.exps rec ssb tsb
Akaike's information criterion for FLSAM	AIC
FLSAM sam variable correlation plot	cor.plot
Drop an element from an FLSAM.control object	drop.from.control
FLR Wrapper for the State-space assessment model (FLSAM)	FLR2SAM FLSAM runSAM SAM2FLR update
FLSAM.control	FLSAM.control
Create FLSAM formatted output file	FLSAM.out sam.out
Class '"FLSAMs"'	FLSAMs FLSAMs-class
Run a sequence of assessments leaving one fleet (non-catch) in or out	loi loo looi
Perform a log-ratio test for all models specified	lr.test
Generate new starting conditions of numbers and f-at-age.	monteCarloStock
North Sea Autumn Spawning Herring Stock Assessment	HERAS.sams NSH NSH.ctrl NSH.sam NSH.tun
Create diagnostic observation variance v.s. CV plot.	obscv.plot
Create diagnostic observation variance plot.	obsvar.plot
Visualise uncertainity in the terminal Fbar and SSB	otolith
Parameter accessor functions for FLSAM	coef coefficients params
Produce diagnostics on process error in the SAM Model	procerr.plot
FLSAM assessment diagnostics	residual.diagnostics
Retrospective stock assessment for FLSAM	retro