R-Package “org” (version 2022.7.20) Published on CRAN

“org” is a system to help you organize projects. Most analyses have three (or more) main sections: code, results, and data, each with different requirements (version control/sharing/encryption). You provide folder locations and ‘org’ helps you take care of the details.

Changes since last version

The R-package “org” (version 2022.7.20) has been published on CRAN. “org” is a part of the splverse, a set of R packages developed to help solve problems that frequently occur when performing infectious disease surveillance. A significant breaking change is that org::initialize_project now takes in env as an argument (the environment into which the functions will be sourced). It is now recommended to include env = .GlobalEnv into the function call.

org::initialize_project(
  env = .GlobalEnv,
  home = "/git/analyses/2019/analysis3/",
  results = "/dropbox/analyses_results/2019/analysis3/"
  raw = "/data/analyses/2019/analysis3/"
)

Concept

The concept behind org is fairly simple - most analyses have three main sections:

• code
• results
• data

Yet each of these sections have extremely different requirements.

Code should:

• Be version controlled
• Be publically accessible
• Have 1 analysis pipeline that logically and sequentially details all steps of the data cleaning, analysis, and result generation

Results should:

• Be immediately shared with close collaborators
• Have each set of results saved and accessible, so that you can see how your results have changed over time (i.e. “if we run the code today, do we get similar results to yesterday?”)

Data should:

• Be encrypted (if sensitive)
• Not stored on the cloud (if sensitive)