New features
- Added
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.
- Added
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 ....
- Added
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.
- Added
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).
- Added
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.
- Added
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.
- Added Palmer Penguins attribution (Horst, Hill & Gorman, 2020)
to the template
.qmd, the create_qmd() roxygen
@details section, and a provenance note in
inst/extdata/.
Breaking changes
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.
New features (continued from
above)
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.- Added
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.
- Added
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.
Bug fixes
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.
Breaking changes
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.
New features
- Added
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/.
Bug fixes
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.
Breaking changes
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.
New features
- Added
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".
- Added
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.
- Added
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.
New features
- Added
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).