# State-Space Assessment Model

## Documentation for package ‘stockassessment’ version 0.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I J L M N O P Q R S T W Y

## -- A --

addforecast | SAM add forecasts
addforecast.samforecast | SAM add forecasts
addRecruitmentCurve | Add stock-recruitment curve to srplot
addRecruitmentCurve.sam | Add stock-recruitment curve to srplot

## -- B --

b0plot | SAM equilibrium biomass in the absence of fishing plot
b0plot.default | SAM equilibrium biomass in the absence of fishing plot
b0plot.hcr | SAM equilibrium biomass in the absence of fishing plot
b0plot.samforecast | SAM equilibrium biomass in the absence of fishing plot
b0table | B0 biomass table
b0table.default | B0 biomass table
bc | Spline basis for use with formula interface

## -- C --

c.sam | Collect sam objects
catchbyfleetplot | SAM catchbyfleet plot
catchbyfleettable | CatchByFleet table
catchplot | SAM catch plot
catchplot.hcr | SAM catch plot
catchplot.sam | SAM catch plot
catchplot.samforecast | SAM catch plot
catchplot.samset | SAM catch plot
catchtable | Catch table
catchtable.sam | 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
componentplot.sam | Area plot of spawning components
corplot | Plots between-age correlations by fleet, either estimated or empirical using residuals.
corplot.sam | Plots between-age correlations by fleet, either estimated or empirical using residuals.
corplot.samres | Plots between-age correlations by fleet, either estimated or empirical using residuals.
corplotcommon | Common function for plotting correlation matrices.

## -- D --

dataplot | SAM Data plot
dataplot.sam | 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

## -- E --

empirobscorrplot | Plots the residual between-age correlation matrices by fleet.
empirobscorrplot.samres | Plots the residual between-age correlation matrices by fleet.
equilibriumbiomassplot | SAM equilibrium biomass plot
equilibriumbiomassplot.default | SAM equilibrium biomass plot
equilibriumbiomassplot.hcr | SAM equilibrium biomass plot
equilibriumbiomassplot.samforecast | SAM equilibrium biomass plot
equilibriumbiomasstable | equilibrium biomass table
equilibriumbiomasstable.default | equilibrium biomass table

## -- F --

faytable | F-at-age table
faytable.sam | F-at-age table
fbarplot | SAM Fbar plot
fbarplot.hcr | SAM Fbar plot
fbarplot.sam | SAM Fbar plot
fbarplot.samforecast | SAM Fbar plot
fbarplot.samset | SAM Fbar plot
fbartable | Fbar table
fbartable.default | Fbar table
fitfromweb | Read a fitted model from stockassessment.org
fitplot | Plots fit to data
fitplot.sam | Plots fit to data
forecast | forecast function to do shortterm
forecastMSY | Estimating Fmsy
forecastMSY.sam | Estimating Fmsy
fselectivityplot | SAM F-selectivity plot
fselectivityplot.sam | SAM F-selectivity plot

## -- G --

generationlengthplot | SAM generation length plot
generationlengthplot.default | SAM generation length plot
generationlengthplot.hcr | SAM generation length plot
generationlengthplot.samforecast | SAM generation length plot
generationlengthtable | Generation length table
generationlengthtable.default | 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

## -- H --

hcr | Harvest control rule forecast
hcr.sam | Harvest control rule forecast

## -- I --

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 ...

## -- J --

jacobian | Calculate jacobian of a function
jit | Jitter runs

## -- L --

leaveout | leaveout run
lifeexpectancyplot | SAM life expectancy plot
lifeexpectancyplot.default | SAM life expectancy plot
lifeexpectancyplot.hcr | SAM life expectancy plot
lifeexpectancyplot.samforecast | SAM life expectancy plot
lifeexpectancytable | Life expectancy table
lifeexpectancytable.default | Life expectancy table
loadConf | Loads a model configuration from a file
logLik.sam | Log likelihood of sam object

## -- M --

modelDescription | Description of model
modelforecast | Model based forecast function
modelforecast.sam | Model based forecast function
modeltable | model table
modeltable.sam | model table
modeltable.samset | model table
modelVersionInfo | Description of model
mohn | Mohn's rho calculation
mohn.samset | Mohn's rho calculation

## -- N --

nobs.sam | Extract number of observations from sam object
nscodConf | nscodConf
nscodData | nscodData
nscodParameters | nscodParameters
ntable | N table
ntable.sam | N table

## -- O --

obscorrplot | Plots the estimated correlation matrices by fleet.
obscorrplot.sam | Plots the estimated correlation matrices by fleet.
obscov | Extract observation covariance matrices from a SAM fit
obscov.sam | Extract observation covariance matrices from a SAM fit
obscov.samset | Extract observation covariance matrices from a SAM fit

## -- P --

parplot | SAM parameter plot
parplot.sam | SAM parameter plot
parplot.samset | SAM parameter plot
partable | parameter table
partable.sam | 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
plotit.hcr | Plot helper
plotit.sam | Plot helper
plotit.samforecast | Plot helper
plotit.samset | Plot helper
predstdplot | Prediction-standard deviation plot
print.hcr | Print hcr object
print.sam | Print sam 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
print.sam_referencepoints | Print referencepoint object
procres | Compute process residuals (single joint sample)

## -- Q --

qtable | table of survey catchabilities
qtable.sam | table of survey catchabilities
qtableplot | plot survey catchabilities
qtableplot.samqtable | plot survey catchabilities

## -- R --

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
recplot.hcr | SAM Recruits plot
recplot.sam | SAM Recruits plot
recplot.samforecast | SAM Recruits plot
recplot.samset | SAM Recruits plot
rectable | Recruit table
rectable.default | Recruit table
reduce | reduce helper function to reduce data
referencepoints | Estimate reference points
referencepoints.sam | 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
retro.sam | retro run
rmaxplot | SAM rmax plot
rmaxplot.default | SAM rmax plot
rmaxplot.hcr | SAM rmax plot
rmaxplot.samforecast | SAM rmax plot
rmaxtable | rmax table
rmaxtable.default | rmax table
rmvnorm | rmvnorm helper function to draw multivariate normal samples
runwithout | runwithout helper function
runwithout.sam | runwithout helper function

## -- S --

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
sdplot.sam | 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
sprplot.default | SAM SPR plot
sprplot.hcr | SAM SPR plot
sprplot.samforecast | SAM SPR plot
sprtable | SPR table
sprtable.default | SPR table
srplot | Plots the stock recruitment
srplot.sam | Plots the stock recruitment
ssbplot | SAM SSB plot
ssbplot.default | SAM SSB plot
ssbplot.hcr | SAM SSB plot
ssbplot.samforecast | SAM SSB plot
ssbtable | SSB table
ssbtable.default | SSB table
stochasticReferencepoints | Estimate stochastic reference points
stochasticReferencepoints.sam | Estimate stochastic reference points
stockassessment-deprecated | Deprecated and defunct functions
summary.sam | Summary of sam object

## -- T --

tableit | Table helper
tableit.sam | Table helper
tableit.samforecast | Table helper
tsbplot | SAM TSB plot
tsbplot.default | SAM TSB plot
tsbtable | TSB table
tsbtable.default | TSB table

## -- W --

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

## -- Y --

yearslostplot | SAM years lost to fishing plot
yearslostplot.default | SAM years lost to fishing plot
yearslostplot.hcr | SAM years lost to fishing plot
yearslostplot.samforecast | SAM years lost to fishing plot
yearslosttable | Years Lost table
yearslosttable.default | Years Lost table
ypr | Yield per recruit calculation
ypr.sam | Yield per recruit calculation
yprplot | SAM YPR plot
yprplot.default | SAM YPR plot
yprplot.hcr | SAM YPR plot
yprplot.samforecast | SAM YPR plot
yprtable | YPR table
yprtable.default | YPR table