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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 |