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 |