Man pages for elisvb/CCAM
Censored Catch Assessment Model
| avail | check availability of certain objects |
| bubble | Bubble plot |
| canmackConf | canmackConf |
| canmackData | canmackData |
| canmackParameters | canmackParameters |
| catchplot | CCAM catch plot |
| catchtable | Catch table |
| ccam.fit | Fit CCAM model |
| c.ccam | Collect ccam objects |
| c.ccamforecast | Collect ccamforecast objects |
| clean.void.catches | remove void catches |
| coef.ccam | Extract fixed coefficients of ccam object |
| copy | copy a list (MPs or OMs) |
| crl | continuous ratio logit transformation of catch-at-age matrix |
| cumsum.bounded | cumsum.bounded |
| defcon | Setup basic minimal configuration for ccam assessment |
| defpar | Setup minimal initial parameters |
| diamondplot | Diamond plots of MSE output |
| expplot | CCAM exploitation rate plot |
| exptable | exploitation rate table |
| extract | extract predictions for a given variable |
| faytable | F-at-age table |
| fbarplot | CCAM fbar plot |
| fbartable | Fbar table |
| fitfromweb | Read a fitted model from stockassessment.org |
| fitplot | fitplot |
| fleet3 | fleet 3 |
| fleet6 | fleet 6 |
| force.fit | Force fit |
| forecast | forecast function to do shortterm |
| foreplot | Plots forecasting results |
| getLowerBounds | Bounds |
| getUpperBounds | Bounds |
| gmean | geometric mean |
| heat | Heat plot |
| IEconstant | IEconstant |
| IEdep0025 | IEdep0025 |
| IEdep2550 | IEdep2550 |
| IEdep5075 | IEdep5075 |
| IEdep75100 | IEdep75100 |
| IEdepcopy | IEdepcopy |
| IEindep1000 | IEindep1000 |
| IEindep2000 | IEindep2000 |
| IEindep2019 | IEindep2019 |
| IEindep3000 | IEindep3000 |
| IEindep4000 | IEindep4000 |
| IEindep4800 | IEindep4800 |
| IEindep500 | IEindep500 |
| IEindep6000 | IEindep6000 |
| IEindep7200 | IEindep7200 |
| IEindepdecr | IEindepdecr |
| IEindepdecrsteep | IEindepdecrsteep |
| IEplot | Plot implementation error |
| invcrl | continuous ratio logit transformed matrix of catches-at-age... |
| invlogit | inverse logit function |
| is.whole.positive.number | Function to test if x is ... |
| jit | Jitter runs |
| jittable | jittable |
| kobeplot | Kobe plot |
| leaveout | leaveout run |
| loadConf | Loads a model configuration from a file |
| logit | logit function |
| logLik.ccam | Log likelihood of ccam object |
| modelDescription | Description of model |
| modeltable | model table |
| modelVersionInfo | Description of model |
| mohn | Mohn's rho calculation |
| MPeggcomplex | MPeggcomplex |
| MPeggcomplex0 | MPeggcomplex0 |
| MPeggcomplex10000 | MPeggcomplex10000 |
| MPeggcomplex15000 | MPeggcomplex15000 |
| MPeggcomplex2000 | MPeggcomplex2000 |
| MPeggcomplex4000 | MPeggcomplex4000 |
| MPeggcomplex6000 | MPeggcomplex6000 |
| MPeggcomplex8000 | MPeggcomplex8000 |
| MPeggcomplexinterim | MPeggcomplexinterim |
| MPeggcomplexramp | MPeggcomplexramp |
| MPeggsimple | MPeggsimple |
| MSEplot | Plot MSE criteria |
| newobs | create new observations (logobs), only for one new year |
| nobs.ccam | Extract number of observations from ccam object |
| nscodConf | nscodConf |
| nscodData | nscodData |
| nscodParameters | nscodParameters |
| ntable | N table |
| onLoad | onload function |
| parplot | CCAM parameter plot |
| partable | parameter table |
| peplot | CCAM PE plot |
| plot.ccam | Plot ccam object |
| plot.ccamforecast | Plot ccamforecast object |
| plot.ccamres | Plot ccam residuals |
| plot.ccamset | Plot ccam object |
| plot.ccamypr | Plot ccam object |
| plot.forecastset | Plot ccamforecast object |
| plotit | Plot helper |
| plotobs | Observation plot |
| prettymatplot | prettymatplot plot |
| print.ccam | Print ccam object |
| print.ccamcoef | Print ccamcoef object |
| print.ccamforecast | Print ccamforecast object |
| print.ccamres | Print ccamres object |
| print.ccamset | Print ccamset object |
| print.ccamypr | Print ccamypr object |
| procres | Compute process residuals (single joint sample) |
| prodplot | Plot surplus production vs SSB |
| raw | extract raw predictions for a given variable |
| read.ices | Function to read ICES/CEFAS data files and validate if input... |
| read.surveys | Function to read ices survey format |
| read.table.nowarn | Function to supress incomplete final line warning |
| recplot | CCAM recruitment plot |
| rectable | Recruit table |
| reduce | reduce helper function to reduce data |
| residuals.ccam | Extract residuals from ccam object |
| resplot | Plots residuals |
| retro | retro run |
| rmvnorm | rmvnorm helper function to draw multivariate normal samples |
| runwithout | runwithout helper function |
| saveConf | Saves a model configuration list to a file |
| savepng | save pngs in one line |
| scplot | CCAM ssb and catch |
| selplot | CCAM selectivity plot |
| seltable | Selectivity table |
| setS | small helper function |
| setSeq | small helper function |
| setup.ccam.data | Combine the data sources to CCAM readable object |
| simulate.ccam | Simulate from a ccam object |
| spay | Standardized proportions at year |
| spya | Standardized proportions at age |
| srplot | Plots the stock recruitment |
| ssb0plot | CCAM SSB0 plot |
| ssb0table | SSB0 table |
| ssbplot | CCAM SSB plot |
| ssbtable | SSB table |
| stepconf | add one year to configuration |
| stepdat | add one year to data |
| steppar | add one year to parameters |
| stick | stick function |
| summary.ccam | Summary of ccam object |
| surveyplot | Plot surveys |
| tableit | Table helper |
| tableset | tableset |
| tsbplot | CCAM TSB plot |
| tsbtable | TSB table |
| ypr | Yield per recruit calculation |
