Stylianos (Stelios) Serghiou, Eirini Tsekitsidou
When we have the preprint or publication, we will post the link here!
Combining resources across OSF and GitHub should yield the following structure.
├── .gitignore <- Lists files to be ignored in syncing between local and remote.
├── LICENSE <- Describes license to the contents of this repo.
├── README.md <- Describes the project and orchestration (how to run)
│
├── data
│ ├── raw <- The original, immutable data dump.
│ │ └── <experiment>
│ │ └── <conditions/replicate>
│ │ └── <date as YYYY-MM-DD>
│ ├── external <- Data from third party sources (e.g., US Census).
│ │ └── <provider>
│ │ └── <date as YYYY-MM-DD>
│ ├── intermediate <- Intermediate data that has been standardized, formatted, deduped, etc.
│ │ └── <experiment>
│ │ └── <conditions/replicate>
│ │ └── <date as YYYY-MM-DD>
│ ├── extracted <- Tabular data extracted from conformed image data.
│ │ └── <experiment>
│ │ └── <conditions/replicate>
│ │ └── <date as YYYY-MM-DD>
│ └── tidy <- The final, canonical datasets for analysis. Includes engineered features.
│ └── <experiment>
│
├── code
│ ├── data-processing <- Code to process data from raw all the way to tidy.
│ │ └── <experiment>
│ ├── draft-analyses <- Code that operates on tidy data for draft data analytics and visualizations.
│ └── final-analyses <- Code that operates on tidy data to produce text, figures and tables as they appear in pubilcations.
│
├── output
│ ├── draft <- Tables and figures from the draft analytics
│ │ └── <experiment>
│ └── final <- Tables and figures from the final analytics
│
├── docs <- Data dictionaries, manuals, and all other explanatory materials.
│
├── publication
│ └── journal <- Journal that this was submitted to
│ └── submission-1_YYYY-MM-DD <- All materials of submission 1
│ ├── docs <- All documents for submission
│ ├── figures <- All figures for submission
│ └── tables <- All tables for submission
│
├── .github
│ ├── linters <- Configuration files for all linters being used
│ └── workflows <- GitHub Actions workflows
│
├── Dockerfile <- Use docker build to build Docker container based on this file
├── deps.R <- Import packages not used elsewhere to help renv
├── renv.lock <- Lockfile with all dependencies managed by renv
└── renv <- Package dependency management directory with renv
All code follows the following structure.
├── Title
│ ├── Inputs <- Define the input sources.
│ └── Outputs <- Define the outputs.
│
├── Setup
│ ├── Import <- Import modules.
│ ├── Parameters <- Input parameters (e.g., data definitions)
│ ├── Configs <- Input any configurations (e.g., source data, % sampled).
│ └── Functions <- Define all functions.
│
├── Read
│ ├── Import <- Import data.
│ └── Conform <- Conform data to a format appropriate for analysis.
│
├── Compute
│ └── Compute - <Analysis type> <- Compute descriptive statistics, visualize, analyze.
│ └── <Analysis subtype> <- Analysis subtype (if applicable; e.g., histograms).
│
├── Write
│ ├── Conform <- Conform data to a format appropriate for storage.
│ └── Export <- Write/push/sink data to a storage service.
│
├── Reproducibility
│ ├── Linting and styling
│ ├── Dependency management
│ └── Containerization
│
├── Documentation
├── Session info
└── References
As of the time of writing, these are on a Share Drive on Google Drive here.
To run this code, use the following diagramatic acyclic graph (DAG). Note that this applies for each experiment. Note that you need to combine all resources first into one repository to run.
To build and run the Docker container, use the following commands in your terminal, executed in the directory containing your Dockerfile (note that Docker needs to be installed and running before you run these commands in your terminal - also, you need to make sure that you have the image by running the following in your terminal: docker pull rocker/r-ver:4.2.3
):
docker build -t calcineurin_image .
docker run calcineurin_image
Then, get the container ID by looking underneath the container name or running
docker ps -a
Finally, retrieve the output:
docker cp -a 355b7a4764f6:/project/code/final_analytics/ code/final_analytics/docker
or
docker cp 355b7a4764f6:/project/code/final_analytics/paper-from-code.html code/final_analytics/paper-from-code_docker.html
If you encounter a bug, please file an issue with a minimal reproducible example here and please Label it as a "bug" (option on the right of your window). For help on how to use the package, please file an issue with a clearly actionable question here and label it as "help wanted." For all other questions and discussion, please email the first author.
- Create an issue as described above.
- Create a branch from the issue as described here.
- Branch names should use the format and voice of this example: "152-bugfix-fix-broken-links".
- Issue a pull request to initiate a review.
- Merge using "Rebase and merge" after you've squashed all non-critical commits.
If you like or are reusing elements of this repo, please give a star!