A Toolkit for Research Workflows.

toolero

toolero is an R package designed to help researchers implement best practices for their coding projects. It provides a small set of opinionated, practical functions that reduce friction at the start of a project and during day-to-day data work.

Installation

You can install toolero from CRAN:

install.packages("toolero")

Or install the development version from GitHub:

# install.packages("pak")
pak::pak("erwinlares/toolero")

Functions

init_project()

Creates a new R project with a standard folder structure suited for research workflows. Optionally initializes renv for package management and git for version control.

library(toolero)

# Create a project with the standard folder structure
init_project(path = "~/Documents/my-project")

# Add extra folders
init_project(path = "~/Documents/my-project",
             extra_folders = c("notebooks", "presentations"))

# Skip renv and git
init_project(path = "~/Documents/my-project", use_renv = FALSE, use_git = FALSE)

The default folder structure includes: data/, data-raw/, R/, scripts/, plots/, images/, results/, and docs/.

create_qmd()

Scaffolds a new Quarto document from a reproducible template, including a sample dataset, UW-Madison branded assets, and an optional post-render purl hook that extracts R code from the rendered document into a companion .R file. Optionally pre-populates the YAML header from a user-supplied YAML config file.

library(toolero)

# Create a document with placeholder YAML
create_qmd(path = "~/Documents/my-project", filename = "analysis.qmd")

# Create without the purl hook
create_qmd(path = "~/Documents/my-project", filename = "report.qmd",
           use_purl = FALSE)

# Pre-populate YAML from a personal config file
create_qmd(path = "~/Documents/my-project", filename = "analysis.qmd",
           yaml_data = "~/my_config.yml")

read_clean_csv()

Reads a CSV file and cleans the column names in one step, producing a tidyverse-friendly tibble.

library(toolero)

data <- read_clean_csv("path/to/file.csv")

# Show column type messages
data <- read_clean_csv("path/to/file.csv", verbose = TRUE)

detect_execution_context()

Identifies which of three execution environments the code is currently running in: an interactive R session, a quarto render call, or a plain Rscript invocation. Returns one of "interactive", "quarto", or "rscript".

library(toolero)

context <- detect_execution_context()

input_file <- switch(context,
  interactive = "data/sample.csv",
  quarto      = params$input_file,
  rscript     = commandArgs(trailingOnly = TRUE)[1]
)

write_by_group()

Splits a data frame by a single grouping column and writes each group to a separate CSV file. Filenames are derived from sanitized group values — converted to lowercase with spaces and special characters replaced by dashes. Optionally writes a manifest.csv listing output files, group values, and row counts.

library(toolero)

# Load the bundled sample dataset
sample_path <- system.file("templates", "sample.csv", package = "toolero")
penguins    <- read_clean_csv(sample_path)

# Split by species
write_by_group(penguins, group_col = "species", output_dir = tempdir())

# Also write a manifest
write_by_group(penguins, group_col = "species",
               output_dir = tempdir(), manifest = TRUE)

generate_kb_xml()

Produces a UW-Madison Knowledge Base importable XML file from a rendered Quarto document. Re-renders the source .qmd with all assets embedded, extracts the HTML body, and wraps it in the KB XML structure along with metadata drawn from the document's YAML header — title → kb_title, description → kb_summary, categories → kb_keywords.

library(toolero)

generate_kb_xml(
  html_path  = "docs/analysis.html",
  output_dir = "exports"
)

When importing the resulting XML into the KB, check the Decode HTML entity in body content option.

Citation

To cite toolero in publications:

citation("toolero")

License

MIT © Erwin Lares.