run_by_group(), the apply half of the split-apply
workflow. Accepts either a manifest CSV produced by
write_by_group(manifest = TRUE) or a named list of data
frames. Applies a user-supplied function to each group subset and
collects the results into a flat tibble (when the function returns a
data frame) or a nested tibble with a list-column (when it returns
anything else). Supports parallel execution via furrr and
future through the workers argument, with a
ceiling at max(1L, parallelly::availableCores() - 1L) to
reserve one core for the main session. A seed argument
enables reproducible parallel execution for analyses involving
randomness.read_clean_csv() for reading CSV files into a
tibble with janitor::clean_names() applied automatically.
Supports explicit missing-value codes via na, selective row
dropping via drop_na (accepts TRUE or a
character vector of column names), an optional ingest summary via
summary, and pass-through arguments to
readr::read_csv() via ....write_clean_csv() for writing data frames to CSV
with clean column names. Applies janitor::clean_names() if
column names are not already clean and reports affected columns via cli
feedback.check_project() for auditing a project directory
against toolero conventions. Checks for expected folders, an
.Rproj file, renv.lock, a git repository, a
README, a .gitignore, and hidden files such as
.RData or .Rhistory. Operates in two modes: a
cli report (default) or a tibble return for programmatic use
(error = FALSE).qmd_to_r() for extracting R code chunks from any
.qmd file into a standalone .R script via
knitr::purl(). The output path defaults to the same
directory as the input with the extension replaced. The
documentation argument controls how much context is
preserved in the extracted script.generate_project_config() for writing a skeleton
YAML project configuration file pre-filled with the standard toolero
folder structure. Intended to be edited by the user and passed to
init_project() via the new config argument.
filename is required and explicit; path
defaults to ".". An overwrite argument
(default FALSE) guards against accidental replacement of an
existing config. The file extension is normalized to .yml
regardless of what is supplied..qmd, the create_qmd() roxygen
@details section, and a provenance note in
inst/extdata/.init_project(): the standard folder structure has been
revised to better reflect research workflow conventions established by
The Carpentries and UW-Madison Libraries. The new standard set is
data-raw/, data/, scripts/,
output/figures/, output/tables/, and
reports/. The previous set (data/,
data-raw/, images/, plots/,
results/, scripts/, docs/,
R/) is no longer created by default.init_project(): extra_folders has been
renamed to custom_folders. The argument now supports a
dplyr-select-like syntax: bare names add folders
(e.g. "models"), names prefixed with "-"
suppress creation of that folder from the resolved set
(e.g. "-output/figures"). Suppression removes only the
named leaf – parent directories are preserved. Duplicate additions emit
an informational message and are skipped; references to non-existent
folders via "-" emit a warning.create_qmd(): no longer copies styles.css
and header.html from the package into the project. Custom
styling is now controlled exclusively by the new use_style
argument. Projects that relied on create_qmd() copying
UW-branded assets should use
init_project(uw_branding = TRUE) to scaffold those files,
then pass use_style = TRUE to create_qmd() to
wire them into the YAML.create_qmd(): sample data is now copied into
data-raw/ instead of data/, consistent with
init_project()’s folder structure.init_project(): added config argument.
When supplied, the folder list in the YAML file replaces the built-in
standard structure entirely. custom_folders is still
applied on top of the config-derived set. Configs are produced by
generate_project_config() and can be stored in the user
home directory for reuse across project types.create_qmd(): added include_examples
argument (default TRUE). When TRUE, copies a
sample dataset (sample.csv) into data-raw/, a
placeholder logo (logo.png) into assets/, and
uses a worked example template with a params block
referencing the sample data. When FALSE, creates a blank
skeleton .qmd with only the YAML header and a setup chunk –
no sample data, no logo, no example analysis block.create_qmd(): added use_style argument
(default FALSE). Accepts FALSE (no custom
styling), TRUE (scans assets/ for
.css and .html files), or a directory path
(scans that directory instead). When exactly one .css file
is found, it is added as css: in the YAML. When exactly one
.html file is found, it is added as
include-before-body:. If multiple files of either type are
found, the function errors and asks the user to specify which one to use
via yaml_data. This decouples styling from
init_project() and supports non-UW branding workflows.inst/templates/skeleton.qmd – a minimal Quarto
template used when include_examples = FALSE. Contains the
YAML header, a setup chunk with library(toolero), and a
single placeholder heading.inst/templates/logo.png – a placeholder logo
image copied into assets/ when
include_examples = TRUE. Reads “your logo goes here” so the
user knows to replace it with their own branding.write_by_group(): group_col now accepts a
character vector of column names, enabling grouping by more than one
column at once. Sanitized filenames join multiple columns with
-- (e.g. group_col = c("species", "sex") on
an Adelie male produces adelie--male.csv); only
combinations actually present in the data produce files, not the full
cross-product of possible values. When manifest = TRUE, the
manifest gains one column per grouping variable (holding the raw,
unsanitized value) in addition to a composite group_value
column joining the raw values with " | ". Single-column
calls are unaffected – filenames, manifest schema, and behavior are
unchanged from previous versions.write_by_group(): added drop_na argument
(default TRUE). Rows with a missing value in any grouping
column are dropped before splitting, with a cli message reporting how
many rows were dropped and from which column(s) – this was previously
silent, undocumented behavior inherited from split(). Set
drop_na = FALSE to instead treat missing values as their
own group rather than dropping them.create_qmd(): use_style = TRUE now
correctly copies rci-banner.png from
inst/assets/ into the project assets/
directory. Previously the banner was only copied inside the
include_examples block and was silently omitted when
use_style = TRUE was combined with
include_examples = FALSE.create_qmd(): filename argument now
normalizes the file extension to .qmd via
fs::path_ext_set(). Passing "my-document" and
"my-document.qmd" both produce
my-document.qmd; a double extension is never added.init_project(): path construction now uses
fs::path() throughout rather than
glue::glue("{path}/{folder}"), ensuring correct behavior on
all platforms.init_project(): branding files are now copied from
inst/assets/ rather than inst/extdata/,
consistent with the rest of the package.create_qmd(): filename is now the first
argument and has no default – it must be supplied explicitly.
path is now the second argument and defaults to
".", allowing natural calls like
create_qmd("analysis.qmd").write_by_group(): sanitized output filenames now use
- (dash) as the separator instead of _
(underscore), consistent with the package convention that file names use
dashes. Existing workflows that reference output paths by name will need
to update accordingly.init_project(): the file_path argument has
been renamed to path for consistency with
create_qmd() and the broader package API. Calls using
file_path = by name will error; positional calls are
unaffected.generate_kb_xml() to produce UW-Madison
KB-importable XML files from rendered Quarto documents. Extracts
metadata from the .qmd YAML header and re-renders with
embedded resources for self-contained import.create_qmd(): added use_purl argument
(default TRUE) that scaffolds a _quarto.yml
post-render hook and a purl.R script for extracting R code
from rendered documents into R/.init_project(): now runs renv::snapshot()
and creates .renvignore after renv::init(),
ensuring the lockfile is populated and .qmd files are
excluded from dependency scanning at project creation time.create_qmd(): _quarto.yml is now copied
from inst/templates/ rather than written from a hardcoded
string, so changes to the template are reflected automatically.create_qmd(): purl.R is now correctly
placed in R/ instead of the project root, consistent with
_quarto.yml calling Rscript R/purl.R.create_qmd(): fixed YAML boolean serialization when
yaml_data is supplied. yaml::as.yaml() was
converting true/false to
yes/no, which Quarto does not recognize. A
custom handler now forces unquoted true/false
output.inst/templates/purl.R: replaced
QUARTO_DOCUMENT_PATH environment variable approach with
fs::dir_ls() glob scan, which works reliably regardless of
how Quarto invokes the post-render script.create_qmd(): path is now a required
argument with no default. Passing NULL or omitting it
raises an error. Use tempdir() for temporary output.write_by_group(): output_dir is now a
required argument with no default. Passing NULL or omitting
it raises an error. Use tempdir() for temporary
output.init_project(): open now defaults to
FALSE instead of TRUE to avoid disrupting the
current RStudio session in non-interactive contexts.detect_execution_context() to identify whether
code is running in an interactive R session, a
quarto render call, or a plain Rscript
invocation. Returns one of "interactive",
"quarto", or "rscript".create_qmd() to scaffold a new Quarto document
from a reproducible template, including a sample dataset, UW-Madison
branded assets, and three-context input resolution via
detect_execution_context(). Optionally pre-populates the
YAML header from a user-supplied YAML config file.write_by_group() to split a data frame by a
single grouping column and write each group to a separate CSV file.
Filenames are derived from sanitized group values. Optionally writes a
manifest.csv listing output files, group values, and row
counts.uw_branding argument to
init_project(). When TRUE, creates an
assets/ folder in the new project and populates it with
UW-Madison RCI branding files (styles.css,
header.html, rci-banner.png).
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