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 |