build(package): ✨ Update package structure according to R CMD CHECK r…

…esutls.

Helps to prepare the package for possible publication in the future.

.Rbuildignore

@@ -6,3 +6,16 @@
 ^LICENSE\.md$
 ^README\.Rmd$
 ^cran-comments\.md$
+^venv$
+^bin$
+^\.python-version$
+^\.github$
+^\.vscode$
+^\.pre-commit-config.yaml$
+^rcmdcheck.log$
+^\.lintr$
+^(inst/)?CITATION(.cff)?$
+^_targets(.R)?$
+^CHANGELOG.md$
+^LICENSE-DOCS$
+^requirements.in$

.Rprofile

@@ -0,0 +1 @@
+source("renv/activate.R")

.lintr

@@ -0,0 +1,4 @@
+linters: linters_with_defaults(
+        indentation_linter = indentation_linter(4)
+    ) # see vignette("lintr")
+encoding: "UTF-8"

.pre-commit-config.yaml

@@ -15,8 +15,9 @@ repos:
 -   repo: https://github.com/lorenzwalthert/precommit
     rev: v0.3.2
     hooks:
+    -   id: readme-rmd-rendered
     -   id: no-browser-statement
     -   id: no-debug-statement
     -   id: parsable-R
+    -   id: use-tidy-description
     -   id: style-files
-    -   id: lintr

DESCRIPTION

@@ -10,13 +10,18 @@ Description: This package bundles the analysis and visualization scripts
     used to process the datasets included for the DSCI 799 capstone project
     for creating predictive models. Datasets must be obtained through external
     sources.
-License: MIT + file LICENSE + file LICENSE-DOCS
+License: MIT + file LICENSE
 URL: https://github.com/rimij405/r-capstone-code
 BugReports: https://github.com/rimij405/r-capstone-code/issues
 Suggests:
+    renv,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 SystemRequirements: python >= 3.12.0 https://www.python.org/downloads/release/python-3120/
+Depends:
+    R (>= 4.3.0)
+Imports:
+    targets

_targets.R

@@ -0,0 +1,62 @@
+# Created by use_targets(). Follow the comments below to fill in this target
+# script. Then follow the manual to check and run the pipeline:
+# https://books.ropensci.org/targets/walkthrough.html#inspect-the-pipeline
+
+# nolint start: commented_code_linter, trailing_whitespace_linter.
+
+# Load packages required to define the pipeline:
+library(targets)
+# library(tarchetypes) # Load other packages as needed.
+
+# Set target options:
+tar_option_set(
+  packages = c("tibble") # packages that your targets need to run
+  # format = "qs", # Optionally set the default storage format. qs is fast.
+  #
+  # For distributed computing in tar_make(), supply a {crew} controller as
+  # discussed at https://books.ropensci.org/targets/crew.html. Choose a
+  # controller that suits your needs. For example, the following sets a
+  # controller with 2 workers which will run as local R processes:
+  #
+  #   controller = crew::crew_controller_local(workers = 2)
+  #
+  # Alternatively, if you want workers to run on a high-performance computing
+  # cluster, select a controller from the {crew.cluster} package. The following
+  # example is a controller for Sun Grid Engine (SGE).
+  #
+  #   controller = crew.cluster::crew_controller_sge( workers = 50, # Many
+  #     clusters install R as an environment module, and you can load it # with
+  #     the script_lines argument. To select a specific verison of R, # you may
+  #     need to include a version string, e.g. "module load R/4.3.0". # Check
+  #     with your system administrator if you are unsure. script_lines = "module
+  #     load R" )
+  #
+  # Set other options as needed.
+)
+
+# tar_make_clustermq() is an older (pre-{crew}) way to do distributed computing
+# in {targets}, and its configuration for your machine is below.
+# options(clustermq.scheduler = "multicore")
+
+# tar_make_future() is an older (pre-{crew}) way to do distributed computing in
+# {targets}, and its configuration for your machine is below. Install packages
+# {{future}}, {{future.callr}}, and {{future.batchtools}} to allow use_targets()
+# to configure tar_make_future() options.
+
+# Run the R scripts in the R/ folder with your custom functions:
+tar_source()
+# source("other_functions.R") # Source other scripts as needed.
+
+# Replace the target list below with your own:
+list(
+  tar_target(
+    name = data,
+    command = tibble(x = rnorm(100), y = rnorm(100))
+    # format = "feather" # efficient storage for large data frames
+  ),
+  tar_target(
+    name = model,
+    command = coefficients(lm(y ~ x, data = data))
+  )
+)
+# nolint end

_targets/.gitignore

@@ -0,0 +1,5 @@
+*
+!.gitignore
+!meta
+meta/*
+!meta/meta

_targets/meta/meta

@@ -0,0 +1,4 @@
+name|type|data|command|depend|seed|path|time|size|bytes|format|repository|iteration|parent|children|seconds|warnings|error
+.Random.seed|object|192e3abaec7d64a5|||||||||||||||
+data|stem|0d3f14a3a96b3ff8|43fae4011a0626f4|ef46db3751d8e999|1588979285||t19697.9230297838s|d07e2e962de596ec|1750|rds|local|vector|||0.006||
+model|stem|1636c25df1da2510|ae83bc723fe2997c|5d1b10f263532bdf|1816327236||t19697.9230298995s|4bab66ba4bee4440|108|rds|local|vector|||0.003||

bin/check

@@ -0,0 +1,21 @@
+#!/usr/bin/env bash
+
+# Installation directory.
+SCRIPT_DIR="$(realpath "${0%/*}")"
+INSTALL_DIR="$(realpath "${SCRIPT_DIR}/../inst")"
+
+# Ensure installation directory exists.
+if [ ! -d "${INSTALL_DIR}" ]; then
+  mkdir -p  "${INSTALL_DIR}"
+fi
+
+# Copy files into the `inst/` directory.
+files=("_targets.R" "CHANGELOG.md" "CITATION" "CITATION.cff")
+
+for file in "${files[@]}"; do
+  cp "${SCRIPT_DIR}/../${file}" "${INSTALL_DIR}/${file}"
+done
+
+# Run check.
+/usr/bin/R --no-echo --no-restore -e "devtools::check()" |
+    tee rcmdcheck.log

bin/run

@@ -0,0 +1,10 @@
+#!/usr/bin/env Rscript
+
+# This is a helper script to run the pipeline.
+# Choose how to execute the pipeline below.
+# See https://books.ropensci.org/targets/hpc.html
+# to learn about your options.
+
+targets::tar_make()
+# targets::tar_make_clustermq(workers = 2) # nolint
+# targets::tar_make_future(workers = 2) # nolint

bin/run-background

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+# <!-- This file was auto-generated by `targets::use_targets()` -->
+
+# Submit the pipeline as a background process with ./run.sh
+# module load R # Uncomment if R is an environment module.
+nohup nice -4 R CMD BATCH ./../run.R &
+
+# Change the nice level above as appropriate
+# for your situation and system.
+
+# Removing .RData is recommended.
+# rm -f .RData

inst/.gitignore

@@ -0,0 +1,4 @@
+_targets.R
+CHANGELOG.md
+CITATION
+CITATION.cff