inst/contribute/copy_ex4.R

In timjmiller/wham: Woods Hole Assessment Model (WHAM)

# after running the example scripts, copy output to correct locations:
#   plot files used by vignettes (vignettes/exY_plots/)
#   data files used by vignettes (data/)
#   test results (inst/extdata/exY_test_results.rds)

# This file uses the 'here' package to work across computers, as long as you 
#   *open from the top-level wham folder* (where you git cloned wham into).
# If you do not have 'here' installed:
# install.packages("here")
library(here)
pkg.dir <- here()
pkgbuild::compile_dll(debug = FALSE); 
pkgload::load_all(compile=FALSE)

# assumes you have a .gitignore'd folder 'sandbox' in the wham folder
# assumes you ran the ex today. if not, need to change
main.dir <- here("sandbox", "pkg_example_results", "ex04")
write.dir <- tempdir(check=TRUE) #will be passed to the ex4_selectivity.R script to set working directory and for writing all results
path_to_scripts <- system.file("example_scripts", package="wham")

#do bias-correction results?
#basic_info <- list(bias_correct_process=TRUE, bias_correct_observation=TRUE) #compare to previous versions

#should write everything to write.dir and create any R objects in the session
source(file.path(path_to_scripts, "ex4_selectivity.R"))

# mod.list <- file.path(write.dir,paste0("m",1:8,".rds"))
# mods <- lapply(mod.list, readRDS)
#vign4_conv <- lapply(mods, function(x) capture.output(check_convergence(x)))
#df.mods <- read.csv(file.path(write.dir,"ex4_table.csv"))

#save(vign4_conv, file=file.path(pkg.dir, "data","vign4_conv.RData"))
vign4_df_mods <- df.mods

#selAA <- lapply(mods, function(x) x$report()$selAA[[1]])
vign4_selAA <- selAA
#save(vign4_selAA, file=file.path(pkg.dir, "data","vign4_selAA.RData"))
save(vign4_selAA, vign4_conv, vign4_df_mods, file=file.path(pkg.dir, "data","vign4_res.RData"))

# copy selAA.png to vignette plots folder
file.copy(from=file.path(write.dir,"selAA.png"), to=file.path(pkg.dir, "vignettes","ex4_plots","selAA.png"), overwrite=T)

# # save results for testing
# ex4_test_results <- list(pars=NULL, nll=NULL)
# ex4_test_results$pars <- lapply(mods, function(x) as.numeric(x$opt$par))
# ex4_test_results$nll <- sapply(mods, function(x) x$opt$objective)
# saveRDS(ex4_test_results, file=file.path(pkg.dir, "inst","extdata","ex4_test_results.rds"))