Package: FLFishery 0.3.8.9009

Iago Mosqueira

FLFishery: Classes and Methods for Simpler Fleet/Fishery Modelling

A set of classes and methods for modelling of fleet dynamics. Fisheries are groups of vessels sharing an effort time series, with static or changing spatio-temporal patterns in selectivity.

Authors:Iago Mosqueira [cre, aut]

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NEWS

# Install 'FLFishery' in R:

install.packages('FLFishery', repos = c('https://ices-tools-prod.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/flr/flfishery/issues

Datasets:

nsfleet - Simulated fisheries data for fisheries exploiting North sea plaice and sole.
ple - Simulated fisheries data for fisheries exploiting North sea plaice and sole.
sol - Simulated fisheries data for fisheries exploiting North sea plaice and sole.

On CRAN:

fisheries flr

59 exports 1.90 score 36 dependencies 7 dependents 7 scripts

Last updated 10 months agofrom:04a563447a. Checks:OK: 1 WARNING: 6. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Sep 01 2024
R-4.5-win	WARNING	Sep 01 2024
R-4.5-linux	WARNING	Sep 01 2024
R-4.4-win	WARNING	Sep 01 2024
R-4.4-mac	WARNING	Sep 01 2024
R-4.3-win	WARNING	Sep 01 2024
R-4.3-mac	WARNING	Sep 01 2024

Exports:as.FLStock capacity capacity<-catch catch.n catch.q catch.q<-catch.sel catch.sel<-catch.wt ccost cost cpue crewshare crewshare<-discards discards.n discards.n<-discards.ratio discards.sel discards.wt discards.wt<-effort effort<-FCB fcb2int fcost fcost<-FLCatch FLCatches FLFisheries FLFishery fwdWindow guessfcb harvest harvests hperiod hperiod<-landings landings.n landings.n<-landings.sel landings.wt landings.wt<-lrevenue model model<-orevenue orevenue<-params params<-price price<-profit propagate show summary vcost vcost<-

Dependencies:cli colorspace cowplot data.table fansi farver FLCore ggplot2 ggplotFL ggrepel glue gridExtra gtable isoband iterators labeling lattice lifecycle magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig R6 RColorBrewer Rcpp rlang scales tibble utf8 vctrs viridisLite withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Create an 'FLStock' object from 'FLBiol' and 'FLFishery' or 'FLFisheries'	as.FLStock,FLBiol-method
Matrix of Fishery - Catch - Biol relationships	FCB,ANY-method FCB,FLBiols-method FCB,FLFisheries-method FCB,missing-method
fcb2int function	fcb2int
FLCatch constructor	catch,FLCatch-method catch.n,FLCatch-method catch.q,FLCatch-method catch.q<-,FLCatch,FLPar-method catch.q<-,FLCatch,numeric-method catch.sel,FLCatch-method catch.sel<- catch.sel<-,FLCatch,FLQuant-method catch.sel<-,FLCatch,numeric-method catch.sel<--method catch.wt,FLCatch-method desc,FLCatch-method desc<-,FLCatch,character-method discards,FLCatch-method discards.n,FLCatch-method discards.n<-,FLCatch,FLQuant-method discards.n<-,FLCatch,numeric-method discards.ratio discards.ratio,FLCatch-method discards.ratio-method discards.sel,FLCatch-method discards.wt,FLCatch-method discards.wt<-,FLCatch,FLQuant-method discards.wt<-,FLCatch,numeric-method FLCatch FLCatch,FLQuant-method FLCatch,missing-method FLCatch-class FLCatch-method FLCatch-methods landings,FLCatch-method landings.n,FLCatch-method landings.n<-,FLCatch,FLQuant-method landings.n<-,FLCatch,numeric-method landings.sel,FLCatch-method landings.wt,FLCatch-method landings.wt<-,FLCatch,FLQuant-method landings.wt<-,FLCatch,numeric-method lrevenue lrevenue,FLCatch-method lrevenue-method name,FLCatch-method name<-,FLCatch,character-method plot,FLCatch,missing-method price,FLCatch-method price<-,FLCatch,FLQuant-method price<-,FLCatch,numeric-method range,FLCatch-method range<-,FLCatch,numeric-method
FLCatches constructor	FLCatches FLCatches,list-method FLCatches,missing-method FLCatches-class FLCatches-methods
FLFisheries constructor	catch,FLFisheries-method catch.n,FLFisheries-method catch.wt,FLFisheries-method discards,FLFisheries-method discards.n,FLFisheries-method FLFisheries FLFisheries,list-method FLFisheries,missing-method FLFisheries-class FLFisheries-methods landings,FLFisheries-method landings.n,FLFisheries-method landings.wt,FLFisheries-method
Classes and Methods for Modeling of Fishing Fleets	capacity capacity,FLFishery-method capacity-method capacity<- capacity<-,FLFishery,FLQuant-method capacity<-,FLFishery,numeric-method capacity<--method catch,FLFishery-method catch.n,FLFishery-method catch.wt,FLFishery-method ccost,FLFishery-method cost,FLFishery-method crewshare crewshare,FLFishery-method crewshare-method crewshare<- crewshare<-,FLFishery,predictModel-method crewshare<--method discards,FLFishery-method discards.n,FLFishery-method effort,FLFishery,ANY-method effort<-,FLFishery,FLQuant-method fcost,FLFishery-method fcost<-,FLFishery,FLQuant-method fcost<-,FLFishery,numeric-method FLFishery FLFishery,FLCatch-method FLFishery,list-method FLFishery,missing-method FLFishery-class FLFishery-method FLFishery-methods hperiod hperiod,FLFishery-method hperiod-method hperiod<- hperiod<-,FLFishery,FLQuant-method hperiod<-,FLFishery,numeric-method hperiod<--method iter,FLFishery-method iter<-,FLFishery,FLFishery-method landings,FLFishery-method landings.n,FLFishery-method landings.wt,FLFishery-method lrevenue,FLFishery-method orevenue orevenue,FLFishery-method orevenue-method orevenue<- orevenue<-,FLFishery,FLQuant-method orevenue<-,FLFishery,numeric-method orevenue<--method profit,FLFishery-method propagate,FLFishery-method revenue,FLFishery-method summary,FLFishery-method vcost,FLFishery-method vcost<-,FLFishery,FLQuant-method [,FLFishery,ANY,missing,ANY-method [[<-,FLFishery,character,missing,FLCatch-method [[<-,FLFishery,numeric,missing,FLCatch-method
An internal class for homogeneous fishing fleets	capacity,FLFisherycpp-method capacity<-,FLFisherycpp,FLQuant-method capacity<-,FLFisherycpp,numeric-method crewshare,FLFisherycpp-method crewshare<-,FLFisherycpp,FLQuant-method crewshare<-,FLFisherycpp,numeric-method effort,FLFisherycpp,ANY-method effort<-,FLFisherycpp,FLQuant-method effort<-,FLFisherycpp,numeric-method fcost,FLFisherycpp-method fcost<-,FLFisherycpp,FLQuant-method fcost<-,FLFisherycpp,numeric-method FLFisherycpp FLFisherycpp-class FLFisherycpp-methods hperiod,FLFisherycpp-method hperiod<-,FLFisherycpp,FLQuant-method hperiod<-,FLFisherycpp,numeric-method orevenue,FLFisherycpp-method orevenue<-,FLFisherycpp,FLQuant-method orevenue<-,FLFisherycpp,numeric-method vcost,FLFisherycpp-method vcost<-,FLFisherycpp,FLQuant-method vcost<-,FLFisherycpp,numeric-method
Generate an FCB matrix from FLBiols and FLFisheries	guessfcb
Methods to calculate fishing mortalities	fbar,FLBiol-method fbar,FLBiols-method harvest harvest,FLBiol,FLCatch-method harvest,FLBiol,FLFisheries-method harvest,FLBiol,FLFishery-method harvest,FLBiols,FLFisheries-method harvest,FLBiols,FLFishery-method harvests harvests,FLBiol,FLFisheries-method harvests-method
Simulated fisheries data for fisheries exploiting North sea plaice and sole.	nsfishery nsfleet ple sol