freeze: Run an analysis while freezing a copy of the code (and...

In ekernf01/freezr: Easily Archive Quickly Changing Custom R Scripts For Reproducible Analysis

Description

Run an analysis while freezing a copy of the code (and perhaps dependencies) for later perusal.

Usage

freeze(
  analyses_to_run,
  prefix_omit = "scripts",
  destination,
  run_from_cryo_storage = FALSE,
  dependencies = NULL,
  seed_to_set = NULL,
  timestamp_as_folder = TRUE,
  force = FALSE,
  copy_deps_kb_limit = 100,
  purl_aggressively = TRUE,
  chastise = FALSE,
  notes_file = "notes.md",
  repos_to_track = NULL
)

Arguments

analyses_to_run	R or R markdown files to be run and frozen.
prefix_omit	freeze archives your code in a way that preserves folder structures, but if you want to omit a prefix, specify it here.
destination	Where to save the code (and log, and maybe dependencies and output)
run_from_cryo_storage	If FALSE (default), runs the code from the current working directory. If TRUE, runs from destination (or a folder within it – see param timestamp_as_folder). The default option, FALSE, makes it easier to write your code because you know where it'll be run from. You can access Sys.getenv()[["FREEZR_DESTINATION"]] within your scripts to produce custom output. The non-default option makes it easier to break code unless it uses absolute paths throughout.
dependencies	A list of file paths to extra files your analysis uses. They will get saved to destination if they are smaller than copy_deps_kb_limit.
seed_to_set	seed for rng. If NULL (default), seed doesn't get set.
timestamp_as_folder	If TRUE (default), one extra folder is added to destination based on the current time and date (down to the second). If FALSE, code gets saved to destination.
force	If FALSE, refuses to continue when destination is not empty. If TRUE, continues saving results even to non-empty destination. Default is FALSE.
copy_deps_kb_limit	dependencies get saved to destination if they are smaller than copy_deps_kb_limit.
purl_aggressively	If TRUE (default), then when purling Rmd files, the corresponding R files may be overwritten.
chastise	If TRUE (default), creates a notes.txt file for you and nags you about filling it.
notes_file	Name of file to be created while chastiseing.
repos_to_track	For git users. If you want to record what commit some outside repo is on – for example, a package that you are developing separate from your data analysis repo – put the path here. You can put more than one.

Value

returns destination arg.

Examples

#setwd( file.path( "~", "my_freezr_example_project" ), )
#freeze( analyses_to_run = c( "scripts/my_functions.Rmd", "scripts/my_script.R" ),
#        destination = file.path("~", "my_freezr_example_project", "results") )

ekernf01/freezr documentation built on Feb. 8, 2022, 5:22 a.m.