State-Space Assessment Model


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Documentation for package ‘stockassessment’ version 0.5.4

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addforecast SAM add forecasts
c.sam Collect sam objects
catchbyfleetplot SAM catchbyfleet plot
catchbyfleettable CatchByFleet table
catchplot SAM catch plot
catchtable Catch table
clean.void.catches remove void catches
coef.sam Extract fixed coefficients of sam object
corplot Plots between-age correlations by fleet, either estimated or empirical using residuals.
corplotcommon Common function for plotting correlation matrices.
defcon Setup basic minimal configuration for sam assessment
defpar Setup minimal initial parameters
empirobscorrplot Plots the residual between-age correlation matrices by fleet.
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
getLowerBounds Bounds
getUpperBounds Bounds
is.whole.positive.number Function to test if x is ...
jit Jitter runs
leaveout leaveout run
loadConf Loads a model configuration from a file
logLik.sam Log likelihood of sam object
modelDescription Description of model
modeltable model table
modelVersionInfo Description of model
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.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
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
procres Compute process residuals (single joint sample)
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
residuals.sam Extract residuals from sam object
retro retro run
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
setS small helper function
setSeq small helper function
setup.sam.data Combine the data sources to SAM readable object
simulate.sam Simulate from a sam object
srplot Plots the stock recruitment
ssbplot SAM SSB plot
ssbtable SSB table
summary.sam Summary of sam object
tableit Table helper
tsbplot SAM TSB plot
tsbtable TSB table
ypr Yield per recruit calculation