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

This document demonstrates how you can use freezr within the layout of a typical data-analysis project.

setwd("path/to/my/project")

# # Load freezr and make a shortcut to cut down on boilerplate
library(freezr)

#' When run without args, this function runs only setup.Rmd, and it saves to the "interactive_results" folder.
#' Otherwise, it runs both setup.Rmd and an analysis script, and it 
#' names the results subfolder after the source code subfolder. This way, the same
#' organizational structure is used for the analysis scripts and the results folders.
#' 
flash_freeze = function( analysis_to_run = NULL, results_subdir = NULL ){
  if(is.null(results_subdir)){
     if(is.null(analysis_to_run)){
      results_subdir = "interactive_results"
    } else {
      results_subdir = "results"
    }
  }
  freezr::freeze( analyses_to_run = file.path( "scripts", c( "setup.Rmd", analysis_to_run )),
                  destination = file.path( getwd(), results_subdir ),
                  chastise = F, seed_to_set = 00000000, 
                  repos_to_track = c("path/to/my/project", "~/path/to/related/coevolving/toolbox") )
}

# This call runs your setup function, after which you can play around with the code.
flash_freeze()
# Clean run goes here.
flash_freeze( "qc_all.Rmd" )

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