File Organization

Jason M. Gleditsch 1

Sebastiano De Bona 2

Mathew R. Helmus 3

Jocelyn E. Behm 4

Last Updated: 07 April 2021

Source: vignettes/110_organization.Rmd

Summary

  • Each project should have a separate folder with at least four subfolders:
    • data
    • submission
    • references
    • R project folder(s)

Proper file organization makes it so that data files are easy to find and their purpose easy to ascertain. Projects should be split into at least four separate folders:

  • data

  • submission

  • references (optional – a Zotero reference library is required instead)

  • code

As stated in the beginning of this DMP, a project should be defined by the data. If you are using data for multiple smaller projects (or manuscripts) then you may have subfolders in the project folder for those smaller projects. However, it is recommended that instead of having subfolders for those projects, you should have separate R projects and, therefore, R project folders, for those smaller projects thereby making a new R package for each subproject/manuscript.

Data Folder

The data folder will hold all of the various data tables, pictures, GIS data, etc. you are using for the project.

Root folder: Only the latest versions of your data should be in the root data folder.

Subfolders:

  • raw: the original data files. These data files should never be edited!

  • old: versions of your data.

You can add more subfolders to better organize your data if you wish.

Note: this data folder is different than the one that will be in your R project folder (see the R Packaging section). The data folder in your R project folder (likely named something like ‘data_raw’) will only hold the data you are using for your analyses. You can use a separate R script to import the latest versions (or a specific version) of your data into this folder overwriting the data already in that folder (see the Useful R Code section). To make this easier, there is a data_import() function being written for the iEcoDMP package (iEcoDMP is currently under construction).

Submission Folder

The submission folder will hold all all of your files you are using for manuscript creation.

Root folder: Files created and used for manuscript creation and presentation

Subfolders:

  • figures: all figure files

  • tables: all tables and appendices for the publication

  • old: older versions of figures, tables and manuscript

References Folder

The references folder will hold any important journal articles you are using for your project.

Subfolders: created based on subject or manuscript

Note: in lieu of this references folder, Zotero reference manager library should be used. See the Reference Libraries section for more information.

Code Folder

The code folder will hold all scripts and R project folder(s).

Subfolders:

  • R Project folders (see R Packaging section)

  • Any scripts that are not ran in R can be in a different subfolder named for the program/language used. However, these scripts can also be in a subfolder of the R project folder to make uploading to github and version controlling with git easier.

Example

Project Root Folder

Code Folder

  • caribmacro and caribnet are R Project folders

  • google_ee is java script code used for Google Earth Engine

Data Folder

Reference Folder

Submission Folder

  • As you can see from the file names, there are 3 different manuscript drafts in the root folder from 2 different subprojects. You can have these like it is shown or you can have separate subfolders for these manuscripts (recommended).

Glossary

References

Additional Resources

  1. Temple University, ↩︎

  2. Temple University, ↩︎

  3. Temple University, ↩︎

  4. Temple University, ↩︎