Package: FLasher 0.7.1.9223
Iago Mosqueira
FLasher: Projection and Forecasting of Fish Populations, Stocks and Fleets
Projection of future population and fishery dynamics is carried out for a given set of management targets. A system of equations is solved, using Automatic Differentation (AD), for the levels of effort by fishery (fleet) that will result in the required abundances, catches or fishing mortalities.
Authors:
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FLasher.pdf |FLasher.html✨
FLasher/json (API)
NEWS
| # Install 'FLasher' in R: |
| install.packages('FLasher', repos = c('https://ices-tools-prod.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/flr/flasher/issues
Last updated 12 days agofrom:e5c5b292a6. Checks:OK: 1 WARNING: 7 ERROR: 1. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 09 2024 |
| R-4.5-win-x86_64 | ERROR | Dec 09 2024 |
| R-4.5-linux-x86_64 | WARNING | Dec 09 2024 |
| R-4.4-win-x86_64 | WARNING | Dec 09 2024 |
| R-4.4-mac-x86_64 | WARNING | Dec 09 2024 |
| R-4.4-mac-aarch64 | WARNING | Dec 09 2024 |
| R-4.3-win-x86_64 | WARNING | Dec 09 2024 |
| R-4.3-mac-x86_64 | WARNING | Dec 09 2024 |
| R-4.3-mac-aarch64 | WARNING | Dec 09 2024 |
Exports:comparedrawFCBFCB<-fwdfwdControlGget_FLQuant_elementget_FLQuant_elementsitersiters<-make_test_operatingModelmatch_posns_namesmergepartialFplotpropagaterandom_FLBiolcpp_generatorrandom_FLCatch_generatorrandom_FLCatches_generatorrandom_FLFisheries_generatorrandom_FLFishery_generatorrandom_FLQuant_generatorrandom_FLQuant_list_generatorrandom_fwdBiols_list_generatorrandom_fwdControl_generatorshowssb_flashstfsummarytargettarget<-
Dependencies:clicolorspacecowplotdata.tablefansifarverFLCoreFLFisheryggplot2ggplotFLggrepelgluegridExtragtableisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerRcpprlangscalestibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Set and replacement accessors for fwdControl | $,fwdControl-method $<-,fwdControl,AsIs-method $<-,fwdControl,vector-method [,fwdControl,ANY,ANY,ANY-method [<-,fwdControl,ANY,ANY,ANY-method [<-,fwdControl,ANY,ANY,vector-method |
| Add the order column to the control target | add_target_order_fls |
| A base class for drawing FCB bits | basicBlock basicBlock-class |
| A class for drawing a biological stock | biolBlock biolBlock-class |
| An FLBiols object used in mixed fishery vignette | biols flfs |
| Calculate fishing mortality | calc_F |
| A class for drawing a catch | catchBlock catchBlock-class |
| Methods for coercing objects between classes | coerce |
| Compare the result of a 'fwd()' run with the defined targets. | compare,FLBiol,fwdControl-method compare,FLStock,fwdControl-method compare,fwdControl,FLStock-method |
| Generic method for drawing components the FCB matrix | draw draw,basicBlock-method draw,biolBlock-method draw,catchBlock-method draw,FCBDrawing-method draw,fisheryBlock-method draw,fwdControl-method draw,matrix-method draw-basicBlock draw-biolBlock draw-catchBlock draw-FCBDrawing draw-fisheryBlock draw-fwdControl draw-matrix draw-method |
| Create and extract the FCB slot in fwdControl | FCB FCB,fwdControl-method FCB<-,fwdControl,matrix-method |
| A class for drawing the FCB matrix | FCBDrawing FCBDrawing,matrix-method FCBDrawing-class FCBDrawing-matrix FCBDrawing-method |
| Fill up character slots | fillchar fillchar,FLBiols-method fillchar,FLFisheries-method |
| A class for drawing a fishery | fisheryBlock fisheryBlock-class |
| Method for running fishery projections | fwd fwd,FLBiol,FLFisheries,fwdControl-method fwd,FLBiol,FLFishery,fwdControl-method fwd,FLBiol,FLFishery,missing-method fwd,FLBiols,FLFisheries,fwdControl-method fwd,FLBiols,FLFisheries,missing-method fwd,FLBiols,FLFishery,fwdControl-method fwd,FLStock,ANY,missing-method fwd,FLStock,missing,fwdControl-method fwd,FLStock,missing,missing-method |
| A class for the targets and limits of a fishery and stock projection. | fwdControl fwdControl,data.frame,array-method fwdControl,data.frame,missing-method fwdControl,data.frame,numeric-method fwdControl,FLQuant,missing-method fwdControl,list,list-method fwdControl,list,missing-method fwdControl,missing,missing-method fwdControl-class fwdControl-methods G |
| Return 1D element index of an FLQuant | get_FLQuant_element |
| Return 1D vector of element indices of an FLQuant | get_FLQuant_elements |
| Make the plug in for inline Cxx | inlineCxxPlugin |
| Access and replace the iters slot of the fwdControl | iters,fwdControl-method iters<- iters<-,fwdControl,array-method |
| Make a test operating model from a single FLStock object | make_test_operatingModel |
| Change names of biols, catches and fisheries in the control object into integer positions | match_posns_names |
| Call the CPP operatingModel run method | operatingModelRun |
| Parse the list argument to fwd to make a fwdControl object | parsefwdList |
| Calculation of fisheries partial fishing mortalities | partialF partialF,FLBiol,FLFisheries-method partialF,FLBiols,FLFisheries-method |
| plot methods that highlight years in fwdControl | plot,FLQuant,fwdControl-method plot,FLQuants,fwdControl-method plot,FLStock,fwdControl-method plot,FLStocks,fwdControl-method |
| Propagate the fwdControl | propagate,fwdControl-method |
| Generate randomly sized and filled FLBiolcpp objects | random_FLBiolcpp_generator |
| Generate randomly sized and filled FLCatch objects | random_FLCatch_generator |
| Generates an FLCatches object - a list of randomly sized and filled FLCatch objects | random_FLCatches_generator |
| Generate a randomly filled and sized FLFisheries object | random_FLFisheries_generator |
| Generate a randomly filled and sized FLFishery object | random_FLFishery_generator |
| Generate randomly sized and filled FLQuant objects | random_FLQuant_generator |
| Generate lists of randomly sized and filled FLQuant objects | random_FLQuant_list_generator |
| Generates a list that can be passed to the CPP fwdBiols constructor | random_fwdBiols_list_generator |
| Random fwdControl object creator | random_fwdControl_generator |
| Show method for fwdControl | show,fwdControl-method |
| Prepare object for future projection | stf stf,FLBiol-method stf,FLStock-method stf,FLStocks-method |
| summary method for fwdControl | summary summary,fwdControl-method |
| Access and replace the target | target target,fwdControl-method target<- target<-,fwdControl,data.frame-method |
| Get the order of targets in a fwdControl | targetOrder |
