A B C D E F G H I J L M N O P Q R S T W Y
addforecast | SAM add forecasts |
addforecast.samforecast | SAM add forecasts |
addRecruitmentCurve | Add stock-recruitment curve to srplot |
addRecruitmentCurve.sam | Add stock-recruitment curve to srplot |
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.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. |
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 |
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 |
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 |
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 |
hcr | Harvest control rule forecast |
hcr.sam | 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 |
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 |
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 |
nobs.sam | Extract number of observations from sam object |
nscodConf | nscodConf |
nscodData | nscodData |
nscodParameters | nscodParameters |
ntable | N table |
ntable.sam | N table |
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 |
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) |
qtable | table of survey catchabilities |
qtable.sam | table of survey catchabilities |
qtableplot | plot survey catchabilities |
qtableplot.samqtable | 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 |
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 |
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 |
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 |
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 |
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 |