Package: mse 2.2.3.9351
Iago Mosqueira
mse: Tools for Running Management Strategy Evaluations using FLR
A set of functions and methods to enable the development and running of Management Strategy Evaluation (MSE) analyses, using the FLR packages and classes and the a4a methods and algorithms.
Authors:
mse_2.2.3.9351.tar.gz
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mse.pdf |mse.html✨
mse/json (API)
NEWS
| # Install 'mse' in R: |
| install.packages('mse', repos = c('https://sprfmo.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/flr/mse/issues
- kobestatistics - Kobe statistics
- oem - S4 class 'FLmse'
- oem - S4 class 'FLmse'
- om - S4 class 'FLmse'
- om - S4 class 'FLmse'
- statistics - Example set of performance statistics
Last updated 2 days agofrom:15f07289c7. Checks:OK: 1 ERROR: 6. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 22 2024 |
| R-4.5-win | ERROR | Nov 22 2024 |
| R-4.5-linux | ERROR | Nov 22 2024 |
| R-4.4-win | ERROR | Nov 22 2024 |
| R-4.4-mac | ERROR | Nov 22 2024 |
| R-4.3-win | ERROR | Nov 22 2024 |
| R-4.3-mac | ERROR | Nov 22 2024 |
Exports:argsargs<-biolbiol<-biolsbiols<-bisectcatchcatch.ncatch.n<-catch.wtcatch.wt<-catch<-catchSSB.hcrcombinationscomputeFp05controlcpue.hcrcpue.inddbdebugdecisionsdefault.oemdepletedeviancesdeviances<-dimsdiscardsdiscards.ndiscards.n<-discards.wtdiscards.wt<-discards<-effort.iseffortlimit.fbestest<-existsexpandGridFCBFCB<-fecfisheriesfisheries<-fixedC.hcrfixedF.hcrfleetBehaviourfleetBehaviour<-FLiemFLmseFLmsesFLoemFLomFLombffwdfwd.omgoFishgridListharvestharvest<-hcrhcr<-hockeystick.hcrhr.hcrhyperstability.fbices.hcrindex.hatindicator.hcrindicator.isinitiateisysisys<-iterlandingslandings<-len.indloadlistmm.spwnm.spwn<-m<-matmat<-mcNmergemeta.estmeta.hcrmethodmethod<-metricsmlc.indmodelmodel<-movingF.hcrmovingF.phcrmpmpa.tmmpCtrlmpDispatchmpsmseCtrlnnoise.iemobservationsobservations<-oemoem<-omom<-perfect.oemperfect.saperformanceperformance<-phcrphcr<-pid.hcrplot_hockeystick.hcrprojectionprojection<-recrefptsrefpts<-response.fbsampling.oemseasonal.isselectMetricsetdeviancesshortcut_devsshortcut.oemshortcut.sasimulatorsp.issplitcatch.issr<-ssbstockstock.nstock.n<-stock.wtstock.wt<-stock<-tac.istarget.hcrtmtm<-track<-trackingtracking<-trend.hcrtsbtunebisecttunegridundebugwt
Dependencies:clicodetoolscolorspacecowplotdata.tabledigestdoFuturefansifarverFLasherFLBRPFLCoreFLFisheryforeachfuturefuture.applyggplot2ggplotFLggrepelglobalsgluegridExtragtableisobanditeratorslabelinglatticelifecyclelistenvmagrittrMASSMatrixmgcvmunsellnlmeparallellypatchworkpillarpkgconfigprogressrR6RColorBrewerRcpprlangscalestibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Bisection search for a forecast target providing a given performance statistic value. | bisect |
| A buffered and non-linear hockeystick HCR | buffer.hcr |
| A HCR to set total catch based on SSB depletion level | catchSSB.hcr |
| Calculates the Fbar value giving a maximum probability of ssb being below Blim of 5% | computeFp05 |
| cpue.hcr | cpue.hcr |
| Creates a single table of output from an FLmse object | db |
| Debugging mse modules | debug,FLo,ANY-method debug,mseCtrl,missing-method debug-mse undebug,FLo,ANY-method undebug,mpCtrl,character-method undebug,mpCtrl,missing-method undebug,mseCtrl,missing-method |
| effort implementation function | effort.is |
| A fixed catch HCR | fixedC.hcr |
| A fixed target f | fixedF.hcr |
| S4 class 'FLiem' | FLiem FLiem-class FLiem-methods initialize,FLiem-method iter,FLiem-method |
| S4 class 'FLmse' | args,FLmse-method args<-,FLmse,list-method control,FLmse-method FLmse FLmse-class FLmse-methods oem oem,FLmse-method oem-methods oem<- oem<--methods om om,FLmse-method om-methods om<- om<--methods tracking tracking,FLmse-method tracking-methods tracking<- tracking<--methods |
| Specification for the observation error model (OEM). | combine,FLoem,FLoem-method deviances,FLoem-method deviances<-,FLoem,list-method FLoem FLoem-class FLoem-methods iter,FLoem-method observations observations,FLoem-method observations-methods observations<- observations<-,FLoem,ANY,FLStock-method observations<-,FLoem,missing,list-method observations<--methods show,FLoem-method |
| A class for an operating model (OM) | combine,FLom,FLom-method control<-,FLmse,mpCtrl-method FLom FLom-class FLom-methods oem<-,FLmse,FLoem-method om<-,FLmse,FLo-method sr,FLom-method sr<-,FLom,FLSR-method stock,FLom-method stock<-,FLom,FLStock-method tracking<-,FLmse,FLQuants-method |
| A method to project the operating model (OM) | fwd.om |
| Functions to create grids and lists of model and simulation runs | expandGrid grid gridList |
| The typical HCR used by ICES | ices.hcr |
| Predicted index of abundance from abundance estimates | index.hat,FLIndexBiomass,FLStock-method |
| An indicator-based HCR | indicator.hcr |
| indicator implementation function | indicator.is |
| Initializes a population for a given virgin biomass. | initiate |
| Kobe statistics | kobestatistics |
| Compute number of necessary Monte Carlo runs | mcN |
| TODO:description | movingF.hcr |
| mp executes a single run of a Management Procedure | mp |
| S4 class 'mpCtrl' | args<-,mpCtrl,function-method args<-,mpCtrl-method debug,mpCtrl,character-method est est,mpCtrl-method est-methods est<- est<-,mpCtrl,function-method est<--methods hcr hcr,mpCtrl-method hcr-methods hcr<- hcr<-,mpCtrl,function-method hcr<--methods initialize,mpCtrl-method isys isys,mpCtrl-method isys-methods isys<- isys<-,mpCtrl,function-method isys<--methods iter,mpCtrl-method iters,mpCtrl-method method,mpCtrl-method method<-,mpCtrl,function-method method<-,mpCtrl-method mpCtrl mpCtrl-class mpCtrl-methods phcr phcr,mpCtrl-method phcr-methods phcr<- phcr<-,mpCtrl,function-method phcr<--methods show,mpCtrl-method tm tm,mpCtrl-method tm-methods tm<- tm<-,mpCtrl,function-method tm<--methods |
| S4 class 'mseCtrl' | args args,mseCtrl-method args-methods args<- args<-,mseCtrl,list-method args<--methods exists exists,mseCtrl-method initialize,mseCtrl-method method method,mseCtrl-method method-methods method<- method<-,mseCtrl,function-method method<--methods mseCtrl mseCtrl-class mseCtrl-methods show,mseCtrl-method |
| FLom object for North sea plaice | p4om |
| A perfect observation of catch and abundances-at-age. | perfect.oem |
| A perfect 'estimate' of abundances, catches and harvest. | perfect.sa |
| Compute performance statistics | performance performance,FLom-method performance,FLStock-method performance,FLStocks-method performance,list-method |
| Samples from an operating model to obtain catch, biology and abundance data | sampling.oem |
| Example set of performance statistics | statistics |
| TAC implementation system module | tac.is |
| Target-based harvest control rule to adjust input or output from CPUE | target.hcr |
| tune | tune |
