State-Space Assessment Model

Documentation for package ‘stockassessment’ version 0.11.0

Help Pages

-- 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

-- C --

c.sam	Collect sam objects
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
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.
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.

-- E --

empirobscorrplot	Plots the residual between-age correlation matrices by fleet.
empirobscorrplot.samres	Plots the residual between-age correlation matrices by fleet.

-- 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 --

getFleet	Extract a fleet from a fitted object
getLowerBounds	Bounds
getUpperBounds	Bounds
grad	Calculate gradient of a function

-- H --

hcr	Harvest control rule forecast

-- I --

Function to test if x is ...

-- J --

jacobian	Calculate jacobian of a function
jit	Jitter runs

-- L --

leaveout	leaveout run
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

-- 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
rmvnorm	rmvnorm helper function to draw multivariate normal samples
runwithout	runwithout helper function

-- S --

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
simstudy	Simulate data from fitted model and re-estimate from each run
simulate.sam	Simulate from a sam object
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
summary.sam	Summary of sam object

-- T --

-- 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 --

ypr	Yield per recruit calculation
ypr.sam	Yield per recruit calculation