In laurieKell/FLCandy: Candidate methods for FLR

library(knitr)
source("R/ini.R")

Required packages

To follow this tutorial you should have installed the following packages:

CRAN:
FLR: FLCore

You can do so as follows:

install.packages(c("iterators"))
install.packages(c("FLCore"), repos="http://flr-project.org/R")

library(devtools)

install_github("lauriekell/FLCandy")

Section

library(plyr)
library(reshape)
library(randtests)

library(FLCore)
library(FLBRP)
library(FLasher)
library(ggplotFL)

library(FLCandy)
library(mydas) 
library(FLife)

data("ple4")
data("ple4brp")

om=fwdWindow(ple4,end=2050,ple4brp)
deviates=rlnoise(100,rec(om)%=%1,0.3,0.7)
om=propagate(om,100)

om.msy=fwd(om,fbar=fbar(om)[,ac(2018:2050)]%=%c(refpts(ple4brp)["msy","harvest"]),sr=ple4brp,residuals=deviates)

om.f01=fwd(om,fbar=fbar(om)[,ac(2018:2050)]%=%c(refpts(ple4brp)["f0.1","harvest"]),sr=ple4brp,residuals=deviates)

om.mey=fwd(om,fbar=fbar(om)[,ac(2018:2050)]%=%c(refpts(ple4brp)["mey","harvest"]),sr=ple4brp,residuals=deviates)

oms=FLStocks("MSY" =om.msy,
              "F0.1"=om.f01,
              "MEY" =om.mey)

plot(oms)

stats=ldply(oms,function(x) omSmry(x,ple4brp))
head(stats)

pMetrics=ddply(stats, .(.id), mydas:::smryStat)
pMetrics

Subsection

More information

To learn more about this subsection, check the FLPKG.

References

@kell2017flr

More information

You can submit bug reports, questions or suggestions on this tutorial at https://github.com/flr/doc/issues.
Alternatively, send a pull request to https://github.com/flr/doc/.
For more information on the FLR Project for Quantitative Fisheries Science in R, visit the FLR webpage: http://flr-project.org.