| SAM add forecasts | addforecast addforecast.samforecast |
| Add stock-recruitment curve to srplot | addRecruitmentCurve addRecruitmentCurve.sam |
| SAM equilibrium biomass in the absence of fishing plot | b0plot b0plot.default b0plot.hcr b0plot.samforecast |
| B0 biomass table | b0table b0table.default |
| Spline basis for use with formula interface | bc |
| Collect sam objects | c.sam |
| SAM catchbyfleet plot | catchbyfleetplot |
| CatchByFleet table | catchbyfleettable |
| SAM catch plot | catchplot catchplot.hcr catchplot.sam catchplot.samforecast catchplot.samset |
| Catch table | catchtable catchtable.sam |
| Catch-at-age in numbers table | caytable |
| remove void catches | clean.void.catches |
| Extract fixed coefficients of sam object | coef.sam |
| Area plot of spawning components | componentplot 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 plot | dataplot dataplot.sam |
| Setup basic minimal configuration for sam assessment | defcon |
| Setup initial values for all model parameters and random effects. | defpar |
| Function to calculate reference points for the embedded deterministic model of a SAM fit | deterministicReferencepoints |
| Function to calculate reference points for the embedded deterministic model of a SAM fit | deterministicReferencepoints.sam |
| Plots the residual between-age correlation matrices by fleet. | empirobscorrplot empirobscorrplot.samres |
| SAM equilibrium biomass plot | equilibriumbiomassplot equilibriumbiomassplot.default equilibriumbiomassplot.hcr equilibriumbiomassplot.samforecast |
| equilibrium biomass table | equilibriumbiomasstable equilibriumbiomasstable.default |
| F-at-age table | faytable faytable.sam |
| SAM Fbar plot | fbarplot fbarplot.hcr fbarplot.sam fbarplot.samforecast fbarplot.samset |
| Fbar table | fbartable fbartable.default |
| Read a fitted model from stockassessment.org | fitfromweb |
| Plots fit to data | fitplot fitplot.sam |
| forecast function to do shortterm | forecast |
| Estimating Fmsy | forecastMSY forecastMSY.sam |
| SAM F-selectivity plot | fselectivityplot fselectivityplot.sam |
| SAM generation length plot | generationlengthplot generationlengthplot.default generationlengthplot.hcr generationlengthplot.samforecast |
| Generation length table | generationlengthtable generationlengthtable.default |
| Update sam fit with additional derived values | getAllDerivedValues |
| Extract a fleet observed or predicted value from a fitted object | getFleet |
| Bounds | getLowerBounds |
| Extract a list of catch fleets | getResidualFleets |
| Bounds | getUpperBounds |
| Calculate gradient of a function | grad |
| Harvest control rule forecast | hcr hcr.sam |
| Integrated spline basis for use with formula interface | ibc |
| Forecast with an ICES advice rule | icesAdviceRule |
| Double integrated spline basis for use with formula interface | iibc |
| Function to test if x is ... | is.whole.positive.number |
| Calculate jacobian of a function | jacobian |
| Jitter runs | jit |
| leaveout run | leaveout |
| SAM life expectancy plot | lifeexpectancyplot lifeexpectancyplot.default lifeexpectancyplot.hcr lifeexpectancyplot.samforecast |
| Life expectancy table | lifeexpectancytable lifeexpectancytable.default |
| Loads a model configuration from a file | loadConf |
| Log likelihood of sam object | logLik.sam |
| Description of model | modelDescription |
| Model based forecast function | modelforecast modelforecast.sam |
| model table | modeltable modeltable.sam modeltable.samset |
| Description of model | modelVersionInfo |
| Mohn's rho calculation | mohn mohn.samset |
| Extract number of observations from sam object | nobs.sam |
| nscodConf | nscodConf |
| nscodData | nscodData |
| nscodParameters | nscodParameters |
| N table | ntable ntable.sam |
| Plots the estimated correlation matrices by fleet. | obscorrplot obscorrplot.sam |
| Extract observation covariance matrices from a SAM fit | obscov obscov.sam obscov.samset |
| SAM parameter plot | parplot parplot.sam parplot.samset |
| parameter table | partable partable.sam |
| Plot hcr object | plot.hcr |
| Plot sam object | plot.sam |
| Plot samforecast object | plot.samforecast |
| Plot sam residuals | plot.samres |
| Plot sam object | plot.samset |
| Plot sam object | plot.samypr |
| Plot by one or two | plotby |
| Plot helper | plotit plotit.hcr plotit.sam plotit.samforecast plotit.samset |
| Prediction-standard deviation plot | predstdplot |
| Print hcr object | print.hcr |
| Print sam object | print.sam |
| Print referencepoint object | print.sam_referencepoints |
| Print samcoef object | print.samcoef |
| Print samforecast object | print.samforecast |
| Print samres object | print.samres |
| Print samset object | print.samset |
| Print samypr object | print.samypr |
| Compute process residuals (single joint sample) | procres |
| table of survey catchabilities | qtable |
| table of survey catchabilities | qtable.sam |
| plot survey catchabilities | qtableplot 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 sense | read.ices |
| Function to read ices survey format | read.surveys |
| Function to supress incomplete final line warning | read.table.nowarn |
| SAM Recruits plot | recplot recplot.hcr recplot.sam recplot.samforecast recplot.samset |
| Recruit table | rectable rectable.default |
| reduce helper function to reduce data | reduce |
| Estimate reference points | referencepoints referencepoints.sam |
| Re-fit a model from stockassessment.org | refit |
| Extract residuals from sam object | residuals.sam |
| retro run | retro retro.sam |
| SAM rmax plot | rmaxplot rmaxplot.default rmaxplot.hcr rmaxplot.samforecast |
| rmax table | rmaxtable rmaxtable.default |
| rmvnorm helper function to draw multivariate normal samples | rmvnorm |
| runwithout helper function | runwithout runwithout.sam |
| Fit SAM model | sam.fit |
| Saves a model configuration list to a file | saveConf |
| Plots the sd of the log observations as estimated in SAM in increasing order | sdplot sdplot.sam |
| small helper function | setS |
| small helper function | setSeq |
| Combine the data sources to SAM readable object | setup.sam.data |
| Simulate data from fitted model and re-estimate from each run | simstudy |
| Simulate from a sam object | simulate.sam |
| SAM SPR plot | sprplot sprplot.default sprplot.hcr sprplot.samforecast |
| SPR table | sprtable sprtable.default |
| Plots the stock recruitment | srplot srplot.sam |
| SAM SSB plot | ssbplot ssbplot.default ssbplot.hcr ssbplot.samforecast |
| SSB table | ssbtable ssbtable.default |
| Estimate stochastic reference points | stochasticReferencepoints stochasticReferencepoints.sam |
| Deprecated and defunct functions | stockassessment-deprecated |
| Summary of sam object | summary.sam |
| Table helper | tableit tableit.sam tableit.samforecast |
| SAM TSB plot | tsbplot tsbplot.default |
| TSB table | tsbtable tsbtable.default |
| Write all data files from a list as created by 'setup.sam.data' | write.data.files |
| Write ICES/CEFAS data file from matrix | write.ices |
| Write surveys in ICES/CEFAS data file from a model object | write.surveys |
| SAM years lost to fishing plot | yearslostplot yearslostplot.default yearslostplot.hcr yearslostplot.samforecast |
| Years Lost table | yearslosttable yearslosttable.default |
| Yield per recruit calculation | ypr ypr.sam |
| SAM YPR plot | yprplot yprplot.default yprplot.hcr yprplot.samforecast |
| YPR table | yprtable yprtable.default |
