master.R

#' A simulation using Multi-species Assessment Method for Alaska (MSAMAK).

#' The simulation includes an operating model and estimation method, which
#' entails an estimation model and one of two data weighting algorithims.
#' The first algorithm is based on McAllister and Ianelli (1997) and the
#' second algorithm is based on Francis (2011) and accounts for correlation.

#' Write more details here.

dirmaster <- file.path("d:", "msamak")
if (!file.exists(dirmaster)) {
  dirmaster <- file.path("c:", "msamak")
}
setwd(dirmaster)

# Label directories
dirmodel <- "model"
dirms <- "ms"
dirom <- "om"
dirsample <- "sample"

library(doParallel)
library(foreach)
library(ggplot2)

ignore <- mapply(source, list.files("R", full.names = TRUE))

#' Copy files from model to OM file
#' The folder "model" holds the parameter estimates used as true
#' values in the simulation
copyfiles <- list.files(dirmodel, full.names = TRUE)
dir.create(dirom)
ignore <- file.copy(copyfiles, dirom, recursive = TRUE)
setwd(dirom)
system(list.files(pattern = "\\.exe"), show.output.on.console = TRUE)
setwd(dirmaster)
assign(dirom, new.env())
attr(om, "name") <- dirom
sys.source(file.path(dirom, "ms.rep"), envir = eval(parse(text = dirom)))

dir.create(dirsample)
setwd(dirsample)
system(list.files(pattern = "\\.exe"), show.output.on.console = TRUE)
setwd(dirmaster)
assign(dirsample, new.env())
attr(sample, "name") <- dirsample
sys.source(file.path(dirsample, "ms.rep"), envir = eval(parse(text = dirsample)))

#' Run the simulation where a single input sample size
#' is used to generate data, but five levels of sample
#' sizes are used for EMs, two above and two below the true.
sim(iteration = 1:5,
  nom = 100, nem = list(1, 100, 200, 1000),
  dirom = "om",
  verbose = FALSE)


#' Create plots
plot_weightatage(file.path(dirms, "weightatage.png"))
plot_sample(environment = om, save = file.path(dirms, "sample.png"),
  width = 7, height = 4)
plot_ts(subset(formatval(getval("Sp_Biom")), em == "om"),
 "Spawning biomass", save = file.path(dirms, "om.png"),
 width = 9, textsize = 15)

plot_ts(formatval(getval("Sp_Biom")), "Spawning biomass",
  save = file.path(dirms, "spb.png"), width = 9)
plot_ts(formatval(getval("pred_rec")), "Recruitment",
  save = file.path(dirms, "rec.png"), width = 9)
plot_ts(formatval(getval("pred_srv")), "Survey", plot.data = NULL,
  save = file.path(dirms, "srv.png"), width = 9)
temp <- formatval(getval("F"))
plot_ts(temp[paste0(temp$age, as.numeric(temp$species)) %in%
  c(161, 162, 132, 133, 134, 135), ], "Fully selected F",
  plot.data = NULL,
  save = file.path(dirms, "f.png"), width = 9)
rm(temp)

plot_sc(formatval(getval("log_Rzero")), "log R_zero",
  save = file.path(dirms, "rzero.png"), width = 9)
plot_sc(formatval(getval("Bzero")), "B_zero",
  save = file.path(dirms, "bzero.png"), width = 9)
plot_sc(formatval(getval("M")), "M",
  save = file.path(dirms, "m.png"), width = 9)
#' End of file.