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