State-Space Assessment Model


[Up] [Top]

Documentation for package ‘stockassessment’ version 0.12.0

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
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
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