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Create a new ggseg atlas package

Source: R/atlas_repo.R
setup_atlas_repo.Rd

Scaffold an R package for distributing a brain atlas. Downloads a modern template from the ggseg-atlas-template GitHub repository and customises it for your atlas. The generated package follows ggseg conventions and includes GitHub Actions workflows, pkgdown configuration, a test suite, and a multi-method scaffold for building your atlas.

Usage

setup_atlas_repo(
  path,
  open = rlang::is_interactive(),
  rstudio = TRUE,
  github_actions = TRUE,
  atlas_name = NULL
)

Arguments

path

Where to create the package. If the directory exists, it must be empty.

open

If TRUE, opens the new project in RStudio. Default is TRUE when running interactively.

rstudio

If TRUE, creates an .Rproj file for RStudio users.

github_actions

If TRUE (default), adds the shared ggsegverse workflows via use_atlas_github_actions().

atlas_name

Name of the atlas (lowercase, no spaces). The package name becomes ggseg{AtlasName}. If NULL, derived from the directory name (e.g., path ggsegDkt becomes atlas name dkt).

Value

Invisibly returns the path to the created package.

Details

The package will be named ggseg{AtlasName} (e.g., ggsegSchaefer for a Schaefer parcellation). After creation, edit the files in data-raw/ to build your atlas, then run devtools::document() and devtools::check().

If the template cannot be downloaded (e.g. no internet), a minimal bundled fallback is used instead. Both paths produce the same GitHub Actions workflows, which are written by use_atlas_github_actions() from templates bundled in this package rather than copied from the atlas template.

DESCRIPTION defaults

The template carries a placeholder author, down to an ORCID of 0000-0000-0000-0000 that roxygen warns about on every render. If you have set the usethis.description option, those fields are written into the new package instead, so you do not retype what R already knows:

options(usethis.description = list(
  "Authors@R" = person(
    "Jane", "Doe",
    email = "jane@example.com",
    role = c("aut", "cre"),
    comment = c(ORCID = "0000-0002-1825-0097")
  ),
  Language = "en-GB"
))

A field the template already declares is replaced; one it does not is added. Package, Title, Description, URL and BugReports are the exceptions – the scaffold derives those from the atlas name, and a stored default would rename the package out from under you.

Examples

if (FALSE) { # \dontrun{
# Create atlas package in a new directory
setup_atlas_repo("ggsegDkt", "dkt")

# Create in current directory, derive name from path
setup_atlas_repo("ggsegMyatlas")

# Specify full path
setup_atlas_repo("~/projects/ggsegSchaefer", "schaefer")

# Without opening in RStudio
setup_atlas_repo("ggsegHarvard", "harvard", open = FALSE)
} # }