reorganize files so available in package

Author: cmlegault

README.md

@@ -9,7 +9,7 @@ library(simASAP)
 simASAP.dir <- find.package("simASAP")
 # replace my directory with one on your computer that you want to use
 my.dir <- "C:\\Users\\chris.legault\\Desktop\\testSimASAP" 
-file.copy(from = file.path(simASAP.dir, "examples", "example_SimASAP.R"), to = my.dir)
+file.copy(from = file.path(simASAP.dir, "example_scripts", "example_SimASAP.R"), to = my.dir)
 ```
 
 <img src="./examples/comparisonplots_simplelogistic.png">

inst/example_scripts/example_SimASAP.R

@@ -0,0 +1,156 @@
+# example_SimASAP.R
+# walks the user through a set of examples
+
+library("simASAP")
+library("ggplot2") # shouldn't need to do this but doesn't seem to work otherwise
+library("dplyr")   # shouldn't need to do this but doesn't seem to work otherwise
+
+# first define where your original ASAP run will be located
+base.dir <- "C:\\Users\\chris.legault\\Desktop\\testSimASAP"
+my.asap.name <- "simplelogistic"
+# assumes you have already run simASAP.dir <- find.package("simASAP")
+file.copy(from = file.path(simASAP.dir, "extdata", paste0(my.asap.name, ".dat")), to = base.dir)
+# get ASAP from the NOAA Fisheries Toolbox and run through the GUI
+
+# now ready to start using simASAP package
+# run SimASAP with defaults to create 10 data sets
+SimASAP(wd=base.dir, asap.name=my.asap.name, nsim=10)
+# the C:\\Users\\chris.legault\\Desktop\\testSimASAP\\sim directory should have been created
+# in this new directory open up two or more of the simplelogistic_simX.dat files
+# and compare the Fleet-1 Catch Data (lines 164-184) and Index-1 and Index-2 Data (lines 281-322)
+# with each other and the original run to see that they have changed
+# can do this by hand or using the ReadASAP3DatFile function
+datorig <- ReadASAP3DatFile(file.path(base.dir, paste0(my.asap.name, ".dat")))
+datsim1 <- ReadASAP3DatFile(file.path(base.dir, "sim", paste0(my.asap.name, "_sim1.dat")))
+datsim2 <- ReadASAP3DatFile(file.path(base.dir, "sim", paste0(my.asap.name, "_sim2.dat")))
+rbind(datorig$dat$CAA_mats[[1]][1, ],
+      datsim1$dat$CAA_mats[[1]][1, ],
+      datsim2$dat$CAA_mats[[1]][1, ])
+# note the original file has the catch at age in proportions (the first 10 columns),
+# while the simulated files have the catch at age in numbers (which will be converted to proportions by ASAP automatically when the program is run)
+
+# now actually run ASAP for a new set of random errors by setting runflag to TRUE
+SimASAP(wd=base.dir, asap.name=my.asap.name, nsim=10, runflag=TRUE)
+# the console should show the simulation number and objective function value
+# it will also show when a particular simulation did not converge
+
+# to see how the results from the simulated data compared to the true values use PlotSimASAP
+PlotSimASAP(wd=base.dir, asap.name=my.asap.name, whichsim=1)
+# this should produce a plot showing Freport, Recruits, and SSB over time
+# comparing the True values and the estimates from the first simulated data set
+
+# to see the results from multiple simulations change whichsim
+PlotSimASAP(wd=base.dir, asap.name=my.asap.name, whichsim=c(1, 3, 5, 7))
+
+# to see the results from all 10 simulations use whichcim=1:10
+PlotSimASAP(wd=base.dir, asap.name=my.asap.name, whichsim=1:10)
+# note the legend is not shown when there are more than five lines plotted
+# the True values are still shown with dots
+
+# to save the plot set save.plots to TRUE
+PlotSimASAP(wd=base.dir, asap.name=my.asap.name, whichsim=1:10, save.plots=TRUE)
+
+# can go wild examining the results, for example,
+# to show just the simulations with the highest and lowest SSB in the terminal year
+res <- PlotSimASAP(wd=base.dir, asap.name=my.asap.name, whichsim=1:10, returnwhat="results")
+mysims <- res %>%
+  filter(Year == max(Year), metric == "SSB", Source != "True") %>%
+  filter(value == min(value) | value == max(value)) %>%
+  mutate(simnum = substr(Source, 4, 99)) %>%
+  select(simnum) %>%
+  unlist(.) %>%
+  as.numeric(.)
+PlotSimASAP(wd=base.dir, asap.name=my.asap.name, whichsim=mysims)
+
+# what if take away a bunch of data and crank up the CVs?
+base.dir <- "C:\\Users\\chris.legault\\Desktop\\testSimASAP"
+my.asap.name <- "badmodel"
+file.copy(from = file.path(simASAP.dir, "examples", paste0(my.asap.name, ".dat")), to = base.dir)
+# need to run badmodel.dat through ASAP GUI before continuing
+SimASAP(wd=base.dir, asap.name=my.asap.name, nsim=10, runflag=TRUE)
+PlotSimASAP(wd=base.dir, asap.name=my.asap.name, whichsim=1:10)
+
+#------------------------------------------------------
+# what if use the wrong M in the simulated input files?
+# this is an advanced use of the package requiring more user coding
+file.copy(from = file.path(base.dir, paste0(my.asap.name, ".dat")),
+          to = file.path(base.dir, "wrongM.dat"))
+file.copy(from = file.path(base.dir, paste0(my.asap.name, ".rdat")),
+          to = file.path(base.dir, "wrongM.rdat"))
+
+wrongM.dir <- file.path(base.dir, "sim", "wrongM")
+if (!dir.exists(wrongM.dir)) dir.create(wrongM.dir)
+file.copy(from = file.path(base.dir, "ASAP3.EXE"),
+          to = file.path(wrongM.dir, "ASAP3.EXE"))
+orig.dir <- getwd()
+setwd(wrongM.dir) # unfortunately need to do this to run ASAP3
+
+for (isim in 1:10){
+  asap.dat <- ReadASAP3DatFile(file.path(base.dir, "sim", paste0(my.asap.name, "_sim", isim, ".dat")))
+  asap.dat$dat$M <- asap.dat$dat$M / 2 # use M=0.15 instead of true M of 0.3
+  wname <- paste0("wrongM_sim", isim)
+  my.bad.name <- file.path(base.dir, "sim", "wrongM", paste0(wname, ".dat"))
+  WriteASAP3DatFile(my.bad.name, asap.dat, "double true M")
+  dname <- paste0(wname, ".dat")
+  file.remove("asap3.rdat")
+  file.remove("asap3.std")
+  shell(paste("ASAP3.exe -ind", dname), intern=TRUE)
+  # use presence of .std file to indicate converged run
+  if (file.exists("asap3.std")){
+    file.copy(from = "asap3.rdat", to =paste0(wname, ".rdat"))
+    asap <- dget("asap3.rdat")
+    objfxn <- asap$like$lk.total
+    print(paste("simulation", isim, "complete, objective function =", objfxn))
+  }else{
+    print(paste("simulation", isim, "did not converge"))
+  }
+}
+setwd(orig.dir)
+wrongM.plot <- PlotSimASAP(base.dir, "wrongM", 1:10, wrongM.dir, FALSE, "plot")
+wrongM.plot <- wrongM.plot + ggtitle("Wrong M (0.15 instead of 0.30) used in assessment")
+ggsave(file = file.path(wrongM.dir, "wrongM.png"), wrongM.plot)
+
+#------------------------------------------------------
+
+# the following lines are just to copy the file into my examples directory and rename
+# file.copy(from = file.path(od, "comparisonplots.png"),
+#           to = paste0("./examples/comparisonplots_", my.asap.name, ".png"))
+# file.copy(from = file.path(base.dir, "simplelogistic.dat"), to = "./examples")
+# file.copy(from = file.path(base.dir, "badmodel.dat"), to = "./examples")
+# file.copy(from = file.path(wrongM.dir, "wrongM.png"), to = "./examples")
+
+# ###################################################################
+# # took a look at a number of actual assessments to see what happens
+# # all this is commented out so users don't try to do it themselves
+# # included here to demonstrate how it can be done
+#
+# # groundfish
+# # ASAP assessment input files from https://www.nefsc.noaa.gov/saw/sasi/sasi_report_options.php
+# base.dir <- "C:\\Users\\chris.legault\\Desktop\\jitter_asap\\"
+# gstocks <- c("gomcod", "gomhaddock", "pollock", "redfish", "snemawinter", "snemayt", "whitehake")
+# nstocks <- length(gstocks)
+# gname <- "base" # did not have to do this, just an easier way of running through many cases in a loop
+#
+# # run each model 10 times
+# for (istock in 1:nstocks){
+#   wd <- file.path(base.dir, gstocks[istock])
+#   SimASAP(wd=wd, asap.name=gname, nsim=10, runflag=TRUE)
+# }
+#
+# # make the plots and modify them to include stock name as title (nice feature of ggplot)
+# gres <- list()
+# for (istock in 1:nstocks){
+#   wd <- file.path(base.dir, gstocks[istock])
+#   myplot <- PlotSimASAP(wd, gname, 1:10, returnwhat="plot")
+#   gres[[istock]] <- myplot + ggtitle(gstocks[istock])
+# }
+# # no indications of problems with any of these
+#
+# pdf(file=file.path(base.dir, "groundfish_comparison_plots.pdf"))
+# for (istock in 1:nstocks){
+#   print(gres[[istock]])
+# }
+# dev.off()
+# file.copy(from=file.path(base.dir, "groundfish_comparison_plots.pdf"), to="./examples")
+#
+