If you run into problems you can contact allen.chen@noaa.gov. This is a work in progress and should not be used for management!
To install:
> install.packages("devtools")
> library(devtools)
Set the directory you've downloaded the package into:
> setwd("J:/Fishperson/Directory_containing_nwblastarca")
Install:
> install("nwblastarca", build_vignettes = FALSE)
You can look at the documentation here:
> help(package = "nwblastarca")
Run through the wrapper function:
> library(nwblastarca)
> firstyear <- 2017
> forecastyrs <- 2
> dynamic.stocks <- c('WA.OR.lingcod')
> MCMC <- 100
> filename <- system.file("extdata/lingcod", package = "nwblastarca")
> WA.OR.lingcod.dynstock <- Read_SS(filename)
> data(StocksRecCatchByArea)
> data(NWdata)
> tsout <- blast_arca_wrapper(MCMC = MCMC, firstyear = firstyear,
forecastyrs = forecastyrs, stocks.rec.catch.by.area = StocksRecCatchByArea,
datain = NWdata, dynamic.stocks = dynamic.stocks,
dynstock = list(WA.OR.lingcod.dynstock = WA.OR.lingcod.dynstock))
If you want to run it in parallel you need to register your workers first, for example:
> library(doParallel)
> registerDoParallel(cores = 8)
> tsout <- blast_arca_wrapper(MCMC = MCMC, firstyear = firstyear,
forecastyrs = forecastyrs, stocks.rec.catch.by.area = StocksRecCatchByArea,
datain = NWdata, dynamic.stocks = dynamic.stocks,
dynstock = list(WA.OR.lingcod.dynstock = WA.OR.lingcod.dynstock),
parallel = TRUE)
Currently outputs numbers at age and recreational catches for the dynamic species, and takes about 16 hours for 100 iterations with 8 workers (on an Intel i7-8700).
We can use the included summary function to plot the results, where you can save the plots to a chosen directory if desired:
> wd <- "J:/Fishperson/Directory_to_save_plots/"
> plotout <- Plot_res(tsout, MCMC, wd = wd, savep = TRUE, samplei = TRUE)
> plotout[[1]]
> dev.new()
> plotout[[2]]
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