Create a minimal targets template in the current project — populate_targets

This function creates a minimal targets template in the current directory. This includes creating a Pipelines.qmd file containing boilerplate for running analyses, and a Results.qmd file which can be used to visualize the results. Parallelization of the pipeline is implemented using targets::tar_make() and crew.cluster, using pre-filled using parameters specific to the LPC system at Penn.

Files are written to path, which defaults to the working directory. Passing it explicitly matters when the project directory holds none of the markers a project search looks for (an .Rproj file, a DESCRIPTION, a git repository, a .vscode/ directory), because such a search otherwise walks up and writes into a parent directory.

The runtime argument selects the R installation the pipeline runs against, and is passed through to use_crew_lsf(). "native", the default, loads the LPC's R module and leaves the package library to renv; "container" instead runs the main targets process and every worker inside the LPC's RStudio Singularity image.

Usage

populate_targets_proj(
  title,
  log_folder = "build_logs",
  path = ".",
  runtime = c("native", "container"),
  overwrite = FALSE
)

Arguments

title: (character) base name for project files (eg. "title-Pipeline.qmd" and "title-Results.qmd")
log_folder: (character) directory for LSF logs
path: (character) project directory the files are written to, defaulting to the working directory
runtime: (character) R runtime the pipeline and its LSF workers use: "native" (the default) for the module-provided R, or "container" for the LPC RStudio Singularity image
overwrite: (logical) replace existing template files without asking first

Examples

if (FALSE) { # \dontrun{
populate_targets_proj("test")
populate_targets_proj("test", runtime = "container")
} # }