Package: stockassessment 0.12.0

stockassessment: State-Space Assessment Model

Fitting SAM...

Authors:Anders Nielsen [aut, cre], Casper Berg [aut], Christoffer Moesgaard Albertsen [aut], Kasper Kristensen [aut], Mollie Brooks [aut], Vanessa Trijoulet [aut], Olav Nikolai Breivik [aut]

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NEWS

# Install 'stockassessment' in R:
install.packages('stockassessment', repos = c('https://fishfollower.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/fishfollower/sam/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

stockassessment

7.63 score 48 stars 2 packages 300 scripts 86 exports 6 dependencies

Last updated 5 hours agofrom:77a6e494c9. Checks:ERROR: 3 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesFAILNov 22 2024
R-4.5-win-x86_64WARNINGNov 22 2024
R-4.5-linux-x86_64WARNINGNov 22 2024
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R-4.4-mac-x86_64WARNINGNov 22 2024
R-4.4-mac-aarch64ERRORNov 22 2024
R-4.3-win-x86_64WARNINGNov 22 2024
R-4.3-mac-x86_64WARNINGNov 22 2024
R-4.3-mac-aarch64ERRORNov 22 2024

Exports:addRecruitmentCurveb0plotb0tablebccatchbyfleetplotcatchbyfleettablecatchplotcatchtablecaytablecomponentplotcorplotcorplotcommondataplotdefcondefpardeterministicReferencepointsempirobscorrplotequilibriumbiomassplotequilibriumbiomasstablefaytablefbarplotfbartablefitfromwebfitplotforecastforecastMSYfselectivityplotgenerationlengthplotgenerationlengthtablegetAllDerivedValuesgetFleetgetResidualFleetshcribciibcjitleaveoutlifeexpectancyplotlifeexpectancytableloadConfmodelDescriptionmodelforecastmodeltablemodelVersionInfomohnntableobscorrplotobscovparplotpartableplotbypredstdplotprocresqtableqtableplotread.data.filesread.icesrecplotrectablereducereferencepointsretrormaxplotrmaxtablermvnormrunwithoutsam.fitsaveConfsdplotsetup.sam.datasimstudysprplotsprtablesrplotssbplotssbtabletsbplottsbtablewrite.data.fileswrite.iceswrite.surveysyearslostplotyearslosttableypryprplotyprtable

Dependencies:ellipselatticeMatrixRcppRcppEigenTMB

Readme and manuals

Help Manual

Help pageTopics
SAM add forecastsaddforecast addforecast.samforecast
Add stock-recruitment curve to srplotaddRecruitmentCurve addRecruitmentCurve.sam
SAM equilibrium biomass in the absence of fishing plotb0plot b0plot.default b0plot.hcr b0plot.samforecast
B0 biomass tableb0table b0table.default
Spline basis for use with formula interfacebc
Collect sam objectsc.sam
SAM catchbyfleet plotcatchbyfleetplot
CatchByFleet tablecatchbyfleettable
SAM catch plotcatchplot catchplot.hcr catchplot.sam catchplot.samforecast catchplot.samset
Catch tablecatchtable catchtable.sam
Catch-at-age in numbers tablecaytable
remove void catchesclean.void.catches
Extract fixed coefficients of sam objectcoef.sam
Area plot of spawning componentscomponentplot componentplot.sam
Plots between-age correlations by fleet, either estimated or empirical using residuals.corplot corplot.sam corplot.samres
Common function for plotting correlation matrices.corplotcommon
SAM Data plotdataplot dataplot.sam
Setup basic minimal configuration for sam assessmentdefcon
Setup initial values for all model parameters and random effects.defpar
Function to calculate reference points for the embedded deterministic model of a SAM fitdeterministicReferencepoints
Function to calculate reference points for the embedded deterministic model of a SAM fitdeterministicReferencepoints.sam
Plots the residual between-age correlation matrices by fleet.empirobscorrplot empirobscorrplot.samres
SAM equilibrium biomass plotequilibriumbiomassplot equilibriumbiomassplot.default equilibriumbiomassplot.hcr equilibriumbiomassplot.samforecast
equilibrium biomass tableequilibriumbiomasstable equilibriumbiomasstable.default
F-at-age tablefaytable faytable.sam
SAM Fbar plotfbarplot fbarplot.hcr fbarplot.sam fbarplot.samforecast fbarplot.samset
Fbar tablefbartable fbartable.default
Read a fitted model from stockassessment.orgfitfromweb
Plots fit to datafitplot fitplot.sam
forecast function to do shorttermforecast
Estimating FmsyforecastMSY forecastMSY.sam
SAM F-selectivity plotfselectivityplot fselectivityplot.sam
SAM generation length plotgenerationlengthplot generationlengthplot.default generationlengthplot.hcr generationlengthplot.samforecast
Generation length tablegenerationlengthtable generationlengthtable.default
Update sam fit with additional derived valuesgetAllDerivedValues
Extract a fleet observed or predicted value from a fitted objectgetFleet
BoundsgetLowerBounds
Extract a list of catch fleetsgetResidualFleets
BoundsgetUpperBounds
Calculate gradient of a functiongrad
Harvest control rule forecasthcr hcr.sam
Integrated spline basis for use with formula interfaceibc
Forecast with an ICES advice ruleicesAdviceRule
Double integrated spline basis for use with formula interfaceiibc
Function to test if x is ...is.whole.positive.number
Calculate jacobian of a functionjacobian
Jitter runsjit
leaveout runleaveout
SAM life expectancy plotlifeexpectancyplot lifeexpectancyplot.default lifeexpectancyplot.hcr lifeexpectancyplot.samforecast
Life expectancy tablelifeexpectancytable lifeexpectancytable.default
Loads a model configuration from a fileloadConf
Log likelihood of sam objectlogLik.sam
Description of modelmodelDescription
Model based forecast functionmodelforecast modelforecast.sam
model tablemodeltable modeltable.sam modeltable.samset
Description of modelmodelVersionInfo
Mohn's rho calculationmohn mohn.samset
Extract number of observations from sam objectnobs.sam
nscodConfnscodConf
nscodDatanscodData
nscodParametersnscodParameters
N tablentable ntable.sam
Plots the estimated correlation matrices by fleet.obscorrplot obscorrplot.sam
Extract observation covariance matrices from a SAM fitobscov obscov.sam obscov.samset
SAM parameter plotparplot parplot.sam parplot.samset
parameter tablepartable partable.sam
Plot hcr objectplot.hcr
Plot sam objectplot.sam
Plot samforecast objectplot.samforecast
Plot sam residualsplot.samres
Plot sam objectplot.samset
Plot sam objectplot.samypr
Plot by one or twoplotby
Plot helperplotit plotit.hcr plotit.sam plotit.samforecast plotit.samset
Prediction-standard deviation plotpredstdplot
Print hcr objectprint.hcr
Print sam objectprint.sam
Print referencepoint objectprint.sam_referencepoints
Print samcoef objectprint.samcoef
Print samforecast objectprint.samforecast
Print samres objectprint.samres
Print samset objectprint.samset
Print samypr objectprint.samypr
Compute process residuals (single joint sample)procres
table of survey catchabilitiesqtable
table of survey catchabilitiesqtable.sam
plot survey catchabilitiesqtableplot qtableplot.samqtable
Read all standard data SAM files and return a list as created by 'setup.sam.data'read.data.files
Function to read ICES/CEFAS data files and validate if input makes senseread.ices
Function to read ices survey formatread.surveys
Function to supress incomplete final line warningread.table.nowarn
SAM Recruits plotrecplot recplot.hcr recplot.sam recplot.samforecast recplot.samset
Recruit tablerectable rectable.default
reduce helper function to reduce datareduce
Estimate reference pointsreferencepoints referencepoints.sam
Re-fit a model from stockassessment.orgrefit
Extract residuals from sam objectresiduals.sam
retro runretro retro.sam
SAM rmax plotrmaxplot rmaxplot.default rmaxplot.hcr rmaxplot.samforecast
rmax tablermaxtable rmaxtable.default
rmvnorm helper function to draw multivariate normal samplesrmvnorm
runwithout helper functionrunwithout runwithout.sam
Fit SAM modelsam.fit
Saves a model configuration list to a filesaveConf
Plots the sd of the log observations as estimated in SAM in increasing ordersdplot sdplot.sam
small helper functionsetS
small helper functionsetSeq
Combine the data sources to SAM readable objectsetup.sam.data
Simulate data from fitted model and re-estimate from each runsimstudy
Simulate from a sam objectsimulate.sam
SAM SPR plotsprplot sprplot.default sprplot.hcr sprplot.samforecast
SPR tablesprtable sprtable.default
Plots the stock recruitmentsrplot srplot.sam
SAM SSB plotssbplot ssbplot.default ssbplot.hcr ssbplot.samforecast
SSB tablessbtable ssbtable.default
Estimate stochastic reference pointsstochasticReferencepoints stochasticReferencepoints.sam
Deprecated and defunct functionsstockassessment-deprecated
Summary of sam objectsummary.sam
Table helpertableit tableit.sam tableit.samforecast
SAM TSB plottsbplot tsbplot.default
TSB tabletsbtable tsbtable.default
Write all data files from a list as created by 'setup.sam.data'write.data.files
Write ICES/CEFAS data file from matrixwrite.ices
Write surveys in ICES/CEFAS data file from a model objectwrite.surveys
SAM years lost to fishing plotyearslostplot yearslostplot.default yearslostplot.hcr yearslostplot.samforecast
Years Lost tableyearslosttable yearslosttable.default
Yield per recruit calculationypr ypr.sam
SAM YPR plotyprplot yprplot.default yprplot.hcr yprplot.samforecast
YPR tableyprtable yprtable.default