onboard

name	onboard
description	Check that all dependencies required to run this template are installed. Verifies R, LaTeX, required packages, and runs a full smoke test of the pipeline.
disable-model-invocation	true
argument-hint	[none required]

Onboard — Template Environment Check

Verify that your machine can run every part of this template: R scripts, figure generation, table generation, and LaTeX compilation. Run all checks, then report everything at once.

---

Step 1: Detect OS

uname -s   # Darwin = macOS, Linux = Linux

On Windows, check for WSL or Git Bash:

cmd.exe /c ver 2>/dev/null || echo "Not Windows CMD"

The detected OS determines the installation suggestions used throughout this report.

---

Step 2: System Tools

Check that the following CLI tools are available:

Tool	Check command	macOS	Linux	Windows
R / Rscript	Rscript --version	brew install r or r-project.org	sudo apt install r-base	Download from r-project.org
pdflatex	pdflatex --version	brew install --cask mactex-no-gui	sudo apt install texlive-full	Install MiKTeX from miktex.org
latexmk	latexmk --version	Included with MacTeX	sudo apt install latexmk	Via MiKTeX console
bibtex	bibtex --version	Included with MacTeX	Included with texlive	Included with MiKTeX
git	git --version	brew install git	sudo apt install git	Download from git-scm.com

---

Step 3: R Packages

Run this snippet to check all packages the template uses:

Rscript -e '
required <- c(
  "data.table",    # fast CSV reading
  "modelsummary",  # regression tables
  "ggplot2"        # figures
)
installed <- rownames(installed.packages())
missing <- setdiff(required, installed)
if (length(missing) == 0) {
  cat("All", length(required), "R packages installed.\n")
} else {
  cat("Missing:", paste(missing, collapse = ", "), "\n")
  cat("Install with: install.packages(c(\"", paste(missing, collapse = "\", \""), "\"))\n", sep = "")
}
'

---

Step 4: LaTeX Packages

Check that the packages used in draft/preamble/packages.tex are available:

kpsewhich natbib.sty booktabs.sty threeparttable.sty microtype.sty \
          amsmath.sty amssymb.sty graphicx.sty hyperref.sty cleveref.sty \
          dsfont.sty pdflscape.sty subcaption.sty caption.sty \
          setspace.sty relsize.sty xcolor.sty footmisc.sty \
          tabularx.sty multirow.sty tablefootnote.sty

Each call should return a file path. Empty output means the package is missing.

• macOS / Linux (TeX Live / MacTeX): tlmgr install <package-name>
• Windows (MiKTeX): packages auto-install on first compile, or use the MiKTeX console

Also verify that the bibliography style ships with the template:

ls draft/informs2014.bst

This file is included in the template repository — it does not need a separate install.

---

Step 5: Template Data Files

Verify that the sample dataset ships with the repository:

ls -lh data/mtcars.csv

This file is tracked in git and should always be present. If missing, run git checkout data/mtcars.csv.

---

Step 6: Output Directories

Check that output directories exist; create them if missing:

mkdir -p draft/figures draft/tables
ls draft/figures draft/tables

---

Step 7: Smoke Test — Run the Full Pipeline

If all tools are present, execute each stage in order:

Stage 1 — Generate tables (main-analysis.R):

Rscript code/main-analysis.R 2>&1

Expected output: draft/tables/summary-statistics.tex and draft/tables/main-results.tex

Stage 2 — Generate figures (visualization.R):

Rscript code/visualization.R 2>&1

Expected output: draft/figures/scatter_mpg_wt.pdf and draft/figures/scatter_mpg_hp.pdf

Stage 3 — Compile the PDF:

cd draft && latexmk -pdf -interaction=nonstopmode main.tex 2>&1 | tail -20

Expected: exit code 0 and draft/main.pdf generated.

ls -lh draft/main.pdf

---

Output Format

Present results as a checklist:

## Onboard Results

### System Tools
- [x] R 4.x.x
- [x] pdflatex (TeX Live / MacTeX / MiKTeX)
- [x] latexmk
- [x] bibtex
- [x] git
- [ ] pdflatex — MISSING  →  brew install --cask mactex-no-gui

### R Packages (3 required)
- [x] 3/3 installed
- [ ] Missing: ggplot2  →  install.packages("ggplot2")

### LaTeX Packages
- [x] All found
- [ ] Missing: cleveref  →  tlmgr install cleveref

### Template Files
- [x] draft/informs2014.bst
- [x] data/mtcars.csv

### Output Directories
- [x] draft/figures/ exists
- [x] draft/tables/ exists

### Smoke Test
- [x] main-analysis.R  →  tables generated
- [x] visualization.R  →  figures generated
- [x] LaTeX compile    →  main.pdf generated (N pages)

### Summary
Ready to work: YES / NO (list any blocking issues)