01-design.R

message(timestamp(quiet = TRUE))
### Project Setup ==================================================================================
library(here)
project_name <- sub("(.*)_*\\..*", "\\1", list.files(here(), pattern = ".Rproj$"))
output_directory <- here("outputs", "01-design")
dir.create(output_directory, recursive = TRUE, showWarnings = FALSE, mode = "0775")


### Load Packages ==================================================================================
suppressPackageStartupMessages({
  # library(ragg)
  # library(ggplot2)
  # library(ggtext)
  # library(patchwork)
  # library(data.table)
})


### Tables and Figures Theme =======================================================================
# options(
#   ggplot2.discrete.colour = function(...) scale_colour_viridis_d(..., begin = 0.15, end = 0.85),
#   ggplot2.discrete.fill = function(...) scale_fill_viridis_d(..., begin = 0.15, end = 0.85),
#   ggplot2.continuous.colour = function(...) scale_colour_viridis_c(..., begin = 0.15, end = 0.85),
#   ggplot2.continuous.fill = function(...) scale_fill_viridis_c(..., begin = 0.15, end = 0.85)
# )
# theme_set(theme_minimal(base_family = "Tex Gyre Termes"))
# theme_update(
#   plot.title.position = "plot",
#   plot.caption.position = "plot",
#   plot.title = element_markdown(),
#   plot.subtitle = element_markdown(face = "italic", size = rel(0.80)),
#   plot.caption = element_markdown(face = "italic", size = rel(0.65)),
#   axis.title.x = element_markdown(),
#   axis.text.x = element_markdown(),
#   axis.title.y = element_markdown(),
#   axis.text.y = element_markdown()
# )


### Functions ======================================================================================


### Analysis =======================================================================================

# Work in progress ...


### Archive ========================================================================================
# if (!Sys.getenv("USER") %in% c("root", "") && file.exists("~/.fex/id")) {
#   local({
#     owd <- getwd()
#     setwd(normalizePath(output_directory))
#     archive_name <- file.path(
#       normalizePath(output_directory),
#       paste0(
#         format(Sys.Date(), format = "%Y%m%d"), "_",
#         project_name, "_",
#         gsub("[0-9]+\\-", "", basename(output_directory)), ".zip"
#       )
#     )
#     zip(archive_name, files = list.files())
#     fex_out <- system(paste("fexsend", archive_name, "."), intern = TRUE)
#     unlink(archive_name)
#     setwd(owd)
#   })
# }


### Set chmod ======================================================================================
Sys.chmod(
  list.files(output_directory, full.names = TRUE),
  mode = "0775", use_umask = FALSE
)
Sys.chmod(
  list.files(output_directory, full.names = TRUE, recursive = TRUE, all.files = TRUE),
  mode = "0775", use_umask = FALSE
)
invisible(system(paste("chgrp -R staff", output_directory), intern = TRUE))


### Complete =======================================================================================
message("Success!", appendLF = TRUE)
message(timestamp(quiet = TRUE))