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]

FLSAM_3.0.0.9005.tar.gz
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FLSAM.pdf |FLSAM.html✨
FLSAM/json (API)

# Install 'FLSAM' in R:

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

Bug tracker:https://github.com/flr/flsam/issues

Datasets:

HERAS.sams - North Sea Autumn Spawning Herring Stock Assessment
NSH - North Sea Autumn Spawning Herring Stock Assessment
NSH.ctrl - North Sea Autumn Spawning Herring Stock Assessment
NSH.sam - North Sea Autumn Spawning Herring Stock Assessment
NSH.tun - North Sea Autumn Spawning Herring Stock Assessment

On CRAN:

4.51 score 4 stars 406 scripts 75 exports 36 dependencies

Last updated 3 months agofrom:c431925dce. Checks:1 OK, 7 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 03 2025
R-4.5-win	WARNING	Mar 03 2025
R-4.5-mac	WARNING	Mar 03 2025
R-4.5-linux	WARNING	Mar 03 2025
R-4.4-win	WARNING	Mar 03 2025
R-4.4-mac	WARNING	Mar 03 2025
R-4.3-win	WARNING	Mar 03 2025
R-4.3-mac	WARNING	Mar 03 2025

Exports:af anf catch.scale catchabilities clean.void.catches coef coefficients comp.plot components components<-conf2ctrl cor.F cor.obs cor.plot ctrl2conf diags drop.from.control f f.var FLSAM FLSAM.control FLSAM.fast FLSAM.MSE FLSAM.out FLSAM2par FLSAM2SAM FLSAMs formatMatrix formatQuant fpart.plot getLowerBounds getUpperBounds info info<-kobeFLSAM kobeFLSamFn loi loo looi lr.test mohns.rho monteCarloStock monteCarloStockMscan n.states n.states<-n.var nlogl nlogl<-nopar nopar<-obs.var obscor.plot obscov obscov<-obscv.plot obsvar.plot otolith plotkobe power.law.exps procerr.plot rec.pars rescov rescov<-residual.diagnostics retro retroParams retroResiduals retroSelectivity sam.fitfast sam.out SAM2FLR SIM2FLR simulate states states<-

Dependencies:cli colorspace ellipse fansi farver FLCore ggplot2 glue gtable isoband iterators labeling lattice lifecycle magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig plot.matrix R6 RColorBrewer Rcpp RcppEigen rlang scales stockassessment tibble TMB utf8 vctrs viridisLite withr

Citation

Development and contributors

Readme and manuals

Help Manual

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

Usage by other packages (reverse dependencies)