Package: mse 2.4.9
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_2.4.9.tar.gz
mse_2.4.9.zip(r-4.7)mse_2.4.9.zip(r-4.6)mse_2.4.9.zip(r-4.5)
mse_2.4.9.tgz(r-4.6-any)mse_2.4.9.tgz(r-4.5-any)
mse_2.4.9.tar.gz(r-4.7-any)mse_2.4.9.tar.gz(r-4.6-any)
mse_2.4.9.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
mse/json (API)
NEWS
| # Install 'mse' in R: |
| install.packages('mse', repos = c('https://ices-tools-prod.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/flr/mse/issues
- oem - S4 class 'FLmse'
- oem - S4 class 'FLmse'
- om - S4 class 'FLmse'
- om - S4 class 'FLmse'
- statistics - A complete set of performance statistics
simulationmsefisheriesflra4amanagement-strategy-evaluation
Last updated from:6c7e813021. Checks:7 WARNING, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | WARNING | 893 | ||
| source / vignettes | OK | 300 | ||
| linux-release-x86_64 | WARNING | 966 | ||
| macos-release-arm64 | WARNING | 572 | ||
| macos-oldrel-arm64 | WARNING | 483 | ||
| windows-devel | WARNING | 1483 | ||
| windows-release | WARNING | 897 | ||
| windows-oldrel | WARNING | 934 | ||
| wasm-release | OK | 137 |
Exports:argsargs<-biolbiol<-biolsbiols<-catchcatch.ncatch.n<-catch.wtcatch.wt<-catch<-combinationscontrolcpue.indcpues.inddebugdecisionsdefault.oemdepletedeviancesdeviances<-dimsdiscardsdiscards.ndiscards.n<-discards.wtdiscards.wt<-discards<-effortlimit.fbestest<-existsFCBFCB<-fecfisheriesfisheries<-fixedC.hcrfixedF.hcrfleetBehaviourfleetBehaviour<-FLiemFLmseFLmsesFLoemFLomFLombffwdfwd.omgoFishharvestharvest<-hcrhcr<-hockeystick.hcrhrhyperstability.fbindex.hatindicator.isinitiateisysisys<-iterlandingslandings<-loadlistmm.spwnm.spwn<-m<-matmat<-mergemethodmethod<-metricsmodelmodel<-movingF.phcrmpmpa.tmmpCtrlmpDispatchmpsmseCtrlnnoise.iemobservationsobservations<-oemoem<-omom<-perfect.oemperfect.saperformanceperformance<-phcrphcr<-plot_hockeystick.hcrprojectionprojection<-recrefptsrefpts<-response.fbsampling.oemseasonal.isselectMetricsetcontrolsetdeviancesshortcut.oemsimulatorsp.issplit.issr<-ssbstatisticsstockstock.nstock.n<-stock.wtstock.wt<-stock<-tac.istmtm<-track<-trackingtracking<-tsbtunebisectundebugwt
Dependencies:clicodetoolscowplotcpp11data.tabledigestdoFuturefarverFLasherFLBRPFLCoreFLFisheryforeachfuturefuture.applyggplot2ggplotFLggrepelglobalsgluegridExtragtableisobanditeratorslabelinglatticelifecyclelistenvMASSMatrixparallellypatchworkprogressrR6RColorBrewerRcpprlangS7scalesvctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Computes CPUE-based Indicators of changes in Stock Abundance | cpue.ind |
| 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 |
| A fixed target C | 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,data.table-method |
| A method to project the operating model (OM) | fwd.om |
| Hockey-stick Harvest Control Rule | hockeystick.hcr |
| hr method for FLombf | hr,FLombf-method |
| Predicted index of abundance from abundance estimates | index.hat,FLIndexBiomass,FLStock-method |
| Indicator Implementation System Module | indicator.is |
| Initializes a population for a given virgin biomass. | initiate |
| mp executes a single run of a Management Procedure | mp |
| S4 class 'mpCtrl' | args,mpCtrl-method args<-,mpCtrl,function-method args<-,mpCtrl-method debug,mpCtrl,character-method est,mpCtrl-method est<- est<-,mpCtrl,function-method est<-,mpCtrl,list-method est<-,mpCtrl,mseCtrl-method est<--methods hcr,mpCtrl-method hcr<- hcr<-,mpCtrl,function-method hcr<-,mpCtrl,list-method hcr<-,mpCtrl,mseCtrl-method hcr<--methods initialize,mpCtrl-method isys,mpCtrl-method isys<- isys<-,mpCtrl,function-method isys<-,mpCtrl,list-method isys<-,mpCtrl,mseCtrl-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,mpCtrl-method phcr<- phcr<-,mpCtrl,function-method phcr<-,mpCtrl,list-method phcr<-,mpCtrl,mseCtrl-method phcr<--methods show,mpCtrl-method tm,mpCtrl-method tm<- tm<-,mpCtrl,function-method tm<-,mpCtrl,list-method tm<-,mpCtrl,mseCtrl-method tm<--methods |
| Title | mpDispatch |
| Run Multiple Management Procedure Scenarios | mps |
| 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 |
| hr | partialHR |
| A perfect observation of catch and abundances-at-age. | perfect.oem |
| A perfect 'estimate' of abundances, catches and harvest. | perfect.sa |
| Compute Performance Statistics for Management Procedure Evaluation | performance performance,FLmse-method performance,FLmses-method performance,FLo-method performance,FLombf-method performance,FLQuants-method performance,FLStock-method performance,FLStocks-method performance,list-method |
| FLom object | plesim |
| sampling.oem | sampling.oem |
| Select and/or Compute a Metric from the _stk_ and _ind_ inputs | selectMetric |
| setcontrol Modify on the fly the arguments on any mpCtrl module | setcontrol |
| Split a biol target across fleets by setting relative 'quant' proportions | split.is |
| A complete set of performance statistics | statistics |
| TAC implementation system module | tac.is |
| Tune Management Procedures Using Bisection Method | tunebisect |
