Package: FLBEIA 1.16.1.19
FLBEIA Team
FLBEIA: Bio-Economic Impact Assessment of Management Strategies using FLR
A simulation toolbox that describes a fishery system under a Management Strategy Estrategy approach. The objective of the model is to facilitate the Bio-Economic evaluation of Management strategies. It is multistock, multifleet and seasonal. The simulation is divided in 2 main blocks, the Operating Model (OM) and the Management Procedure (MP). In turn, each of these two blocks is divided in 3 components: the biological, the fleets and the covariables on the one hand, and the observation, the assessment and the advice on the other.
Authors:
FLBEIA_1.16.1.19.tar.gz
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FLBEIA.pdf |FLBEIA.html✨
FLBEIA/json (API)
NEWS
| # Install 'FLBEIA' in R: |
| install.packages('FLBEIA', repos = c('https://flr.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/flr/flbeia/issues
- catch - FLBEIA datasets
- evhoe - FLBEIA datasets
- multiAdv - FLBEIA datasets
- multiAdvC - FLBEIA datasets
- multiAssC - FLBEIA datasets
- multiBD - FLBEIA datasets
- multiBio - FLBEIA datasets
- multiBioC - FLBEIA datasets
- multiCv - FLBEIA datasets
- multiCvC - FLBEIA datasets
- multiFl - FLBEIA datasets
- multiFlC - FLBEIA datasets
- multiMainC - FLBEIA datasets
- multiObsC - FLBEIA datasets
- multiRes - FLBEIA datasets
- multiSR - FLBEIA datasets
- oneAdv - FLBEIA datasets
- oneAdvC - FLBEIA datasets
- oneAssC - FLBEIA datasets
- oneBio - FLBEIA datasets
- oneBioC - FLBEIA datasets
- oneCv - FLBEIA datasets
- oneCvC - FLBEIA datasets
- oneFl - FLBEIA datasets
- oneFlC - FLBEIA datasets
- oneIndAge - FLBEIA datasets
- oneIndBio - FLBEIA datasets
- oneItAdv - FLBEIA datasets
- oneItAdvC - FLBEIA datasets
- oneItAssC - FLBEIA datasets
- oneItBio - FLBEIA datasets
- oneItBioC - FLBEIA datasets
- oneItCv - FLBEIA datasets
- oneItCvC - FLBEIA datasets
- oneItFl - FLBEIA datasets
- oneItFlC - FLBEIA datasets
- oneItIndAge - FLBEIA datasets
- oneItIndBio - FLBEIA datasets
- oneItMainC - FLBEIA datasets
- oneItObsC - FLBEIA datasets
- oneItObsCIndAge - FLBEIA datasets
- oneItObsCIndBio - FLBEIA datasets
- oneItRes - FLBEIA datasets
- oneItSR - FLBEIA datasets
- oneMainC - FLBEIA datasets
- oneObsC - FLBEIA datasets
- oneObsCIndAge - FLBEIA datasets
- oneObsCIndBio - FLBEIA datasets
- oneRes - FLBEIA datasets
- oneSR - FLBEIA datasets
Last updated 4 months agofrom:3936481dc2. Checks:ERROR: 1 WARNING: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Nov 14 2024 |
| R-4.5-win-x86_64 | WARNING | Nov 14 2024 |
| R-4.5-linux-x86_64 | WARNING | Nov 14 2024 |
| R-4.4-win-x86_64 | WARNING | Nov 14 2024 |
| R-4.4-mac-x86_64 | WARNING | Nov 14 2024 |
| R-4.4-mac-aarch64 | WARNING | Nov 14 2024 |
| R-4.3-win-x86_64 | WARNING | Nov 14 2024 |
| R-4.3-mac-x86_64 | WARNING | Nov 14 2024 |
| R-4.3-mac-aarch64 | WARNING | Nov 14 2024 |
Exports:addFLCatchadvSumadvSumQaneHCREannexIVHCRannualTACB_flbeiabiolfleets2flstockbioSumbioSumQbrpssonC_flbeiacalculate.q.sel.flrObjscatchNamescatchNames<-catchStockcatchStock.fcatchWStockcatchWStock.fCFPMSYHCRcheckAdvicecheckBDscheckBiolscheckFLBEIADatacheckFleetscheckObsctrlcheckSRscosts_flbeiacreate.advice.ctrlcreate.advice.datacreate.assess.ctrlcreate.BDs.datacreate.biol.arrayscreate.biols.ctrlcreate.biols.datacreate.covars.ctrlcreate.ecoDatacreate.fleets.arrayscreate.fleets.ctrlcreate.fleets.datacreate.indices.datacreate.obs.ctrlcreate.SRs.dataD_flbeiadiscStockdiscStock.fdiscWStockdiscWStock.fecoSum_damaraextractBRPF_flbeiaF2CatchHCRFLBDsimFLBEIAFLCatchesExtFLCatchExtFLFleetExtFLFleetsExtFLMetierExtFLMetiersExtFLSRsimfltStkSumfltStkSumQfltSumfltSumQFroeseHCRghlHCRIcesHCRis.FLCatchesExtis.FLFleetsExtis.FLMetiersExtjoinIterL_flbeialandStocklandStock.flandWStocklandWStock.flittle2011HCRMAPHCRmtStkSummtStkSumQmtSummtSumQMultiStockHCRneaMAC_ltmpnpvnpvQpidHCRpidHCRItargplotbioSumplotBRPssonplotEcoplotFLBiolsplotFLFleetsplotfltStkSumplotfltSumprice_flbeiaR_flbeiarevenue_flbeiariskSumsegregmixSelAtAgesetUnitsNASSB_flbeiastock.fleetInfosummary_flbeiatdiscStocktlandStocktotfcost_flbeiatotvcost_flbeiaunit2ageupdateFLBiolsvesselStkSumvesselStkSumQvesselSumvesselSumQwtadStockwtalStockxtabs2
Dependencies:ADGofTestarrayhelpersaskpassassertthatbackportsbase64encbitbit64blobbroombslibcachemcallrcellrangerclicliprcodacolorspaceconflictedcopulacpp11crayoncurldata.tableDBIdbplyrdeldirdfidxdigestdplyrdtplyrevaluatefansifarverfastmapFLa4aFLashFLAssessFLCoreFLFleetFLXSAfontawesomeforcatsFormulafsgarglegenericsggplot2gluegoogledrivegooglesheets4gridExtragslgtablehavenhighrhmshtmltoolshttridsinterpisobanditeratorsjpegjquerylibjsonliteknitrlabelinglatticelatticeExtralifecyclelmtestlubridatemagrittrMASSMatrixmemoisemgcvmimemlogitmodelrmunsellmvtnormnlmenloptrnumDerivopensslpcaPPpillarpkgconfigplyrpngprettyunitsprocessxprogresspspsplinepurrrR6raggrappdirsrbibutilsRColorBrewerRcppRcppEigenRdpackreadrreadxlrematchrematch2reprexrlangrmarkdownrstudioapirvestsassscalesselectrstablediststatmodstringistringrsvUnitsyssystemfontstextshapingtibbletidyrtidyselecttidyversetimechangetinytextriangletzdbutf8uuidvctrsviridisLitevroomwithrxfunxml2yamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Harvest Control Rules (HCRs) | aneHCRE annexIVHCR annualTAC CFPMSYHCR F2CatchHCR FroeseHCR ghlHCR IcesCat3HCR IcesCat3HCR_bsafe_hrcap IcesHCR little2011HCR MAPHCR MultiStockHCR neaMAC_ltmp pidHCR pidHCRItarg |
| Function to generate an FLStock from an FLBiol and FLFleet | biolfleets2flstock |
| Summary of the FLBEIA output | advSum advSumQ bioSum bioSumQ fltStkSum fltStkSumQ fltSum fltSumQ mtStkSum mtStkSumQ mtSum mtSumQ npv npvQ riskSum vesselStkSum vesselStkSumQ vesselSum vesselSumQ |
| Reference points for a seasonal model | brpsson |
| Calculates selectivity-related parameters | calculate.q.sel.flrObjs |
| Checking inputs of FLBEIA function | checkAdvice checkBDs checkBiols checkFLBEIAData checkFleets checkObsctrl checkSRs |
| advice.ctrl object creator | create.advice.ctrl |
| FLBEIA easy conditioning: advice argument creator | create.advice.data |
| assess.ctrl object creator | create.assess.ctrl |
| FLBEIA easy conditioning: BDs argument creator | create.BDs.data |
| Function to generate an FLBiol object given inputs as arrays | create.biol.arrays |
| biols.ctrl object creator | create.biols.ctrl |
| FLBEIA easy conditioning: biols argument creator | create.biols.data |
| covars.ctrl object creator | create.covars.ctrl |
| Function to generate the covar object neccesary to compute economic indicators and fills in economic slots in FLFleets object | create.ecoData |
| Function to generate an FLFleetsExt object given inputs as arrays | create.fleets.arrays |
| fleets.ctrl object creator | create.fleets.ctrl |
| FLBEIA easy conditioning: fleets argument creator | create.fleets.data |
| FLBEIA easy conditioning: indices argument creator | create.indices.data |
| obs.ctrl object creator | create.obs.ctrl |
| FLBEIA easy conditioning: SRs argument creator | create.SRs.data |
| FLBEIA datasets | catch datasets evhoe multi multiAdv multiAdvC multiAssC multiBD multiBio multiBioC multiCv multiCvC multiFl multiFlC multiMainC multiObsC multiRes multiSR mur one oneAdv oneAdvC oneAssC oneBio oneBioC oneCv oneCvC oneFl oneFlC oneIndAge oneIndBio oneIt oneItAdv oneItAdvC oneItAssC oneItBio oneItBioC oneItCv oneItCvC oneItFl oneItFlC oneItIndAge oneItIndBio oneItMainC oneItObsC oneItObsCIndAge oneItObsCIndBio oneItRes oneItSR oneMainC oneObsC oneObsCIndAge oneObsCIndBio oneRes oneSR res_flbeia |
| Biological summary functions | B_flbeia C_flbeia D_flbeia ecoSum_damara F_flbeia L_flbeia R_flbeia SSB_flbeia summary_flbeia |
| Extracts reference points (specifically Bpa, Blim, Bmsy, Fpa, Flim and Fmsy) from advice.ctrl object, If not available, then values are set to NA. | extractBRP |
| FLBDsim class and methods | FLBDsim FLBDsim-class |
| Run the FLBEIA bio-economic simulation model | FLBEIA |
| Class FLCatchesExt | catchNames,FLCatchesExt catchNames,FLCatchesExt-method catchNames,FLFleetExt catchNames,FLFleetExt-method catchNames,FLFleetsExt catchNames,FLFleetsExt-method catchNames,FLMetierExt catchNames,FLMetierExt-method catchNames,FLMetiersExt catchNames,FLMetiersExt-method FLCatchesExt FLCatchesExt,ANY FLCatchesExt,ANY-method FLCatchesExt,list FLCatchesExt,list-method FLCatchesExt,missing FLCatchesExt,missing-method FLCatchesExt-class is.FLCatchesExt is.FLCatchesExt,ANY is.FLCatchesExt,ANY-method vFLCs |
| FLCatchExt class and the methods to construct it. | addFLCatch,FLCatchExt,FLCatchExt addFLCatch,FLCatchExt,FLCatchExt-method catchNames,FLCatchExt catchNames,FLCatchExt-method catchNames<- catchNames<-,FLCatchExt,character catchNames<-,FLCatchExt,character-method FLCatchExt FLCatchExt,FLQuant-method FLCatchExt,missing-method FLCatchExt-class FLCatchExt-methods FLCatchExt-missing FLQuant,FLCatchExt-method [,FLCatchExt,ANY,ANY,ANY-method [<-,FLCatchExt,ANY,ANY,ANY-method [<-,FLCatchExt,ANY,ANY,FLCatchExt-method |
| FLFleetExt class and the methods to construct it. | FLFleetExt FLFleetExt,FLCatchesExt-method FLFleetExt,FLCatchExt-method FLFleetExt,FLFleetExt-method FLFleetExt,FLFleetExt-missing FLFleetExt,FLMetierExt-method FLFleetExt,FLMetiersExt-method FLFleetExt,missing-method FLFleetExt-class FLFleetExt-methods [,FLFleetExt,ANY,ANY,ANY-method [,FLFleetExt,ANY,ANY-method [,FLFleetExt,ANY,missing,ANY-method [,FLFleetExt,ANY,missing-method [[,FLFleetExt,ANY,missing-method |
| Class FLFleetsExt | FLFleetsExt FLFleetsExt,ANY FLFleetsExt,ANY-method FLFleetsExt,FLFleetExt-missing FLFleetsExt,list FLFleetsExt,list-method FLFleetsExt,missing-method FLFleetsExt-class is.FLFleetsExt is.FLFleetsExt,ANY is.FLFleetsExt,ANY-method vFLFs |
| FLMetierExt class and the methods to construct it. | FLMetierExt FLMetierExt,FLCatchesExt-method FLMetierExt,FLCatchExt-method FLMetierExt,FLMetierExt-method FLMetierExt,FLQuant-method FLMetierExt,missing-method FLMetierExt-class FLMetierExt-methods FLMetiersExt,FLMetiersExt-methods [,FLMetierExt,ANY,missing,ANY-method [,FLMetierExt,ANY,missing-method [[,FLMetierExt,ANY,missing-method |
| Class FLMetiersExt | FLMetiersExt FLMetiersExt,ANY FLMetiersExt,ANY-method FLMetiersExt,is.FLMetiersExt FLMetiersExt,is.FLMetiersExt,ANY FLMetiersExt,list FLMetiersExt,list-method FLMetiersExt,missing FLMetiersExt,missing-method FLMetiersExt-class is.FLMetiersExt is.FLMetiersExt,ANY-method vFLMs |
| FLSRsim class and methods | FLSRsim FLSRsim-class |
| Joins the iterations of several FLBEIA outputs | joinIter |
| Summary plots of the FLBEIA output | plotbioSum plotfltSum |
| YPR plots for a seasonal model | plotBRPsson |
| Plots with fleets data | plotEco |
| Plots with biological data | plotFLBiols |
| Plots with fleets data | plotFLFleets |
| Plots with fltStkSum data | plotfltStkSum |
| Economic summary functions. | costs_flbeia price_flbeia revenue_flbeia totfcost_flbeia totvcost_flbeia |
| Stock-Recruitment models in FLBEIA: segrexmix - Mixture of 2 segmented regression stock-recruitment models fit | segregmix segremix |
| Estimate selectivity at age | SelAtAge |
| Method setUnitsNA | setUnitsNA setUnitsNA,FLBiol-method setUnitsNA,FLBiols-method setUnitsNA,FLFleetExt-method setUnitsNA,FLFleetsExt-method setUnitsNA-methods |
| stock.fleetInfo | stock.fleetInfo |
| Extract landings, discard or catch at age | catchStock catchStock.f catchWStock catchWStock.f discStock discStock.f discWStock discWStock.f landStock landStock.f landWStock landWStock.f tdiscStock tlandStock |
| Translates unit dimension in an FQuant into age dimension | unit2age |
| Update the FLBiols object to the FLCore 2.6 | updateFLBiols |
| Mean weight at age in discards for a stock across fleets and metiers | wtadStock |
| Mean weight at age in landings for a stock across fleets and metiers | wtalStock |