R/populate_package.R

In IBAHCM/RPiR: Reproducible Programming in R

#' populate_package
#'
#' This function will create an RStudio project and populate it with
#' `0105-run-birth-death.R`, and `0105-step-birth-death.R`.
#'
#' @param force - overwrite existing files if TRUE (default FALSE)
#'
#' @export
#'
populate_package <- function(force = FALSE) {
  project_name <- rstudioapi::getActiveProject()
  if (is.null(project_name))
    stop("You are not in an active RStudio project, please create one first")
  package_name <- basename(project_name)

  # Remove R/hello.R
  for (file in c("R/hello.R", "man/hello.Rd", "NAMESPACE")) {
    if (unlink(file) == 0)
      usethis::ui_done(paste("Deleted", usethis::ui_value(file)))
    else
      usethis::ui_oops(paste("Failed to delete", usethis::ui_value(file)))
  }

  # Create demo/ directory
  demo.dir <- "demo"
  if (dir.create(demo.dir, showWarnings = FALSE))
    usethis::ui_done(paste("Creating", usethis::ui_path(demo.dir)))

  # Write demo
  filepath <- file.path(demo.dir, "d0105_run_birth_death.R")
  if (!(file.exists(filepath)) || force) {
    cat("#' # Simple birth-death difference equation model",
        file = filepath)
    tmp <- list("\n",
                "\nlibrary(RPiR)",
                paste0("\nlibrary(", package_name, ")"),
                "\n#' Set up the simulation parameters",
                "\n# Set the birth and death rates",
                "\nbirth.rate <- 0.2",
                "\ndeath.rate <- 0.1",
                "\n",
                "\n# Starting population size",
                "\ninitial.count <- 1",
                "\n",
                "\n# And setting times",
                "\nstart.time <- 0",
                "\nend.time <- 100",
                "\n",
                "\n#' Run the simulation",
                "\n",
                "\n## Set up the population starting size (at the first timestep)",
                "\npopulation.df <- data.frame(count = initial.count)",
                "\n",
                "\n## the timesteps that the simulation will run through",
                "\ntimesteps <- seq(from = start.time + 1, to = end.time)",
                "\n",
                "\n## Now we loop through the time itself (starting at the second timestep)",
                "\nfor (new.time in timesteps) {",
                "\n  updated.population <-",
                "\n    step_deterministic_birth_death(latest = tail(population.df, 1),",
                "\n                                   birth.rate = birth.rate,",
                "\n                                   death.rate = death.rate)",
                "\n  population.df <- rbind(population.df, updated.population)",
                "\n}",
                "\n",
                "\n#' And plot the results",
                "\npopulation.df$time <- c(start.time, timesteps)",
                "\nplot_populations(population.df)",
                "\n")
    lapply(tmp, function(x) cat(x, file = filepath, append = TRUE))
    usethis::ui_done(paste("Writing", usethis::ui_value(filepath)))
  } else {
    usethis::ui_oops(paste("File already exists:", usethis::ui_value(filepath)))
  }

  # Write demo index file
  tmp <- "d0105_run_birth_death   Simple birth-death difference equation model\n"
  index <- file.path("demo", "00Index")
  if (!(file.exists(index)) || force) {
    cat(tmp, file = index)
    usethis::ui_done(paste("Writing", usethis::ui_value(index)))
  } else {
    usethis::ui_oops(paste("File already exists:", usethis::ui_value(index)))
  }

  # Write function
  tmp <- system.file("dummy_package/step_deterministic_birth_death.R",
                     package = "RPiR")
  func.file <- file.path("R", "step_deterministic_birth_death.R")
  if (!(file.exists(func.file)) || force) {
    file.copy(tmp, func.file, overwrite = force)
    usethis::ui_done(paste("Writing", usethis::ui_value(func.file)))
  } else {
    usethis::ui_oops(paste("File already exists:", usethis::ui_value(func.file)))
  }

  # Write githubusername-package file
  filename <- paste0(package_name, "-package.R")
  filepath <- file.path("R", filename)
  if (!(file.exists(filepath)) || force) {
    cat(paste0("#' ", package_name), file = filepath)
    tmp <- list("\n#'",
                paste0("\n#' \\code{", package_name,
                       "} is a dummy package containing a simple birth-death"),
                "\n#' difference equation model.",
                "\n#'",
                "\n#' @author",
                "\n#' Sonia Mitchell <sonia.mitchell@glasgow.ac.uk> (maintainer) \\cr",
                "\n#' Richard Reeve <richard.reeve@glasgow.ac.uk>",
                "\n#'",
                paste0("\n#' @name ", package_name, "-package"),
                paste0("\n#' @aliases ", package_name),
                "\n#' @docType package",
                "\n#'",
                "\n#' @import RPiR",
                "\n#'",
                "\n#' @examples",
                "\n#' \\dontrun{",
                "\n#' # To run the demo",
                paste0("\n#' demo(\"d0105_run_birth_death\", package = \"",
                       package_name, "\")"),
                "\n#' }",
                "\n#'",
                "\nNULL",
                "\n")
    lapply(tmp, function(x) cat(x, file = filepath, append = TRUE))
    usethis::ui_done(paste("Writing", usethis::ui_value(filepath)))
  } else {
    usethis::ui_oops(paste("File already exists:", usethis::ui_value(filepath)))
  }
  # Add dependencies
  usethis::use_dev_package("RPiR", "Imports", remote = "SBOHVM/RPiR")

  # Document package
  devtools::document(quiet = TRUE)
  usethis::ui_done("Documenting package functions")
}