This blog post has also been posted here.
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)