analysis/drake.R

In ashiklom/fortebaseline: Forest Resilience and Threshold Experiment (FoRTE) ED2 baseline runs source code and manuscript

#!/usr/bin/env Rscript
if (getRversion() >= "3.6") {
  options(conflicts.policy = "strict")
  conflictRules("testthat", exclude = "matches")
  conflictRules("drake", exclude = c("gather", "expand", "plan"))
  conflictRules("dplyr",
                mask.ok = c("filter", "lag", "intersect",
                            "setdiff", "setequal", "union"))
  conflictRules("lubridate",
                mask.ok = c("as.difftime", "date"),
                exclude = c("intersect", "setdiff", "union", "here",
                            "stamp"))
  conflictRules("data.table", exclude = c("between", "first", "last",
                                          "transpose", "hour", "isoweek",
                                          "mday", "minute", "month",
                                          "quarter", "second", "wday", "week",
                                          "yday", "year"))
} else {
  warning("Package conflict resolution requires R >= 3.6. ",
          "This script may not work as expected.",
          immediate. = TRUE)
}

suppressPackageStartupMessages({
  library(drake)
  # Data processing
  library(data.table)
  library(dplyr)
  library(tidyr)
  library(forcats)
  library(purrr)
  library(lubridate)
  library(readr)
  # Parallel execution
  library(future)
  library(future.callr)
  library(furrr)
  # Files and file paths
  library(fs)
  library(fst)
  library(here)
  # Plotting
  library(ggplot2)
  library(ggrepel)
  library(cowplot)
})

pkgload::load_all(here::here(), attach_testthat = FALSE)
expose_imports(fortebaseline)

cmdargs <- commandArgs(trailingOnly = TRUE)

# Set common directories and paths
analysis_dir <- here("analysis")
stopifnot(dir_exists(analysis_dir))
data_dir <- dir_create(path(analysis_dir, "data"))
download_dir <- dir_create(path(data_dir, "retrieved"))
fig_dir <- dir_create(path(analysis_dir, "figures"))
drake_dir <- path(analysis_dir, "drake")
stopifnot(dir_exists(drake_dir))

plan <- drake_plan()
src_files <- dir_ls(drake_dir, regexp = "zzskip", invert = TRUE)
walk(src_files, source)

# Parallelism is based on `future`. Parallelism method can be set by adding code
# like the following to .Rprofile-local:
#     future::plan(future::multicore)
# Default method is "sequential"; i.e. no parallelism.

dargs <- list(plan = plan, parallelism = "future", jobs = availableCores())

if ("make" %in% cmdargs) {
  message("Running `drake::make`")
  do.call(drake::make, dargs)
} else if (!interactive()) {
  do.call(drake::config, dargs)
}