Save outputs in the project — save

These functions standardize how outputs are saved in an lbstproj project:

save_data() saves a data frame as rds to data/processed.
save_table() saves a table as rds to data/tables and optionally export it as docx to results/tables.
save_figure() saves a figure as png (or another extension) to results/figures.

To save another R object (e.g. a model, a mice object, ...) to file, use base::saveRDS. By convention, save it to data/<subdir>/ where <subdir> matches the subdirectory in R/ where the script lives. For example, a model created in R/models/ should be saved to data/models/. When using create_file() with a custom type, the matching data/<subdir>/ directory is created automatically.

Each function saves the object using the given name, after validating it. Names can only contain letters, numbers, and hyphens.

Usage

save_data(
  data,
  name,
  overwrite = TRUE,
  quiet = getOption("lbstproj.quiet", FALSE)
)

save_table(
  table,
  name,
  export = TRUE,
  overwrite = TRUE,
  quiet = getOption("lbstproj.quiet", FALSE),
  ...
)

save_figure(
  figure,
  name,
  extension = "png",
  width = 6,
  height = 4,
  overwrite = TRUE,
  quiet = getOption("lbstproj.quiet", FALSE),
  ...
)

Arguments

data

A data.frame to save.

name

Character. File name without extension.

overwrite

Logical. If TRUE, overwrite an existing file with the same name. If FALSE, an error is thrown when the target file already exists.

Default: TRUE. Outputs are overwritten by default.

quiet

Logical. If TRUE, suppress informational messages.

Default: FALSE unless the global option lbstproj.quiet is set otherwise. The default option can be changed using options(lbstproj.quiet = TRUE)

table

A gt_tbl object to save.

export

Logical. If TRUE, also export the table as a .docx file.

Default: TRUE. Word tables are always produced unless specified otherwise.

...

Additional arguments passed to the saving function:

For save_table(): passed to gt::gtsave
For save_figure(): passed to ggplot2::ggsave

figure

A ggplot object to save.

extension

Character. Output format for figures: "png" or "pdf".

Default: "png"

width, height

Numeric. Width and height of the saved figure in inches.

Default: A width of 6 and a height of 4. This fits nicely on a portrait A4 page.

Value

Invisibly returns the path of the saved file.

Examples

if(FALSE) {
  save_data(mtcars, name = "analysis_dataset")

  summary_table <- gt::gt(head(mtcars))
  save_table(summary_table, name = "baseline_characteristics")

  scatter_plot <- ggplot2::ggplot(
    mtcars,
    ggplot2::aes(wt, mpg)
  ) +
    ggplot2::geom_point()
  save_figure(scatter_plot, name = "mpg_vs_weight")
}