iddconf_epiverse

:package: reproducible code principles

https://github.com/mbkoltai/iddconf_epiverse

Repository

:package: reproducible code principles

README.Rmd

---
output: github_document
---




```{r, include = FALSE}
knitr::opts_chunk$set(collapse  = TRUE,
                      comment   = "#>",
                      fig.path  = "man/figures/",
                      out.width = "100%")
```


# IDDconf_epiverse



[![License: GPL (>= 2)](https://img.shields.io/badge/License-GPL%20%28%3E%3D%202%29-blue.svg)](https://choosealicense.com/licenses/gpl-2.0/)
[![Dependencies](https://img.shields.io/badge/dependencies-6/96-orange?style=flat)](#)



Research Compendium of the project **{{ PLEASE ADD A FEW WORDS }}**



### How to cite

Please cite this compendium as: 

> **{{ PLEASE ADD A CITATION }}**



### Content

This repository is structured as follow:

- [`data/`](https://github.com/mbkoltai/IDDconf_epiverse/tree/master/data):
contains all raw data required to perform analyses

- [`analyses/`](https://github.com/mbkoltai/IDDconf_epiverse/tree/main/analyses/):
contains R scripts to run each step of the workflow

- [`outputs/`](https://github.com/mbkoltai/IDDconf_epiverse/tree/main/outputs):
contains all the results created during the workflow

- [`figures/`](https://github.com/mbkoltai/IDDconf_epiverse/tree/main/figures):
contains all the figures created during the workflow

- [`R/`](https://github.com/mbkoltai/IDDconf_epiverse/tree/main/R):
contains R functions developed especially for this project

- [`man/`](https://github.com/mbkoltai/IDDconf_epiverse/tree/main/man):
contains help files of R functions

- [`DESCRIPTION`](https://github.com/mbkoltai/IDDconf_epiverse/tree/main/DESCRIPTION):
contains project metadata (author, date, dependencies, etc.)

- [`make.R`](https://github.com/mbkoltai/IDDconf_epiverse/tree/main/make.R):
main R script to run the entire project by calling each R script stored in the `analyses/` folder



### Usage

Clone the repository, open R/RStudio and run:

```{r eval = FALSE}
source("make.R")
```



### Notes

- All required packages, listed in the `DESCRIPTION` file, will be installed (if necessary)
- All required packages and R functions will be loaded
- Some analyses listed in the `make.R` might take time


### Contributing

Contributions are always welcome!

See our [Contributing guide](/.github/CONTRIBUTING.md) for ways to get started.

Please adhere to this project's [Code of Conduct](/.github/CODE_OF_CONDUCT.md).

### Support

Please see our [Getting help guide](/.github/SUPPORT.md) for support.

### Other notes

use https://readme.so/editor to create/edit README files

general principles can be found in the paper [Good enough practices in scientific computing](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005510)

Owner

Citation (CITATION.cff)

# -----------------------------------------------------------
# CITATION file created with {cffr} R package, v0.5.0
# See also: https://docs.ropensci.org/cffr/
# -----------------------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "IDDconf_epiverse" in publications use:'
type: software
license: GPL-2.0-or-later
title: 'IDDconf_epiverse: Reproducible code'
version: 0.0.0.9000
abstract: A paragraph providing a full description of the project (on several lines...)
authors:
- family-names: Koltai
  given-names: Mihaly
  email: kolmisi@gmail.com
repository-code: https://github.com/mbkoltai/IDDconf_epiverse
url: https://github.com/mbkoltai/IDDconf_epiverse
contact:
- family-names: Koltai
  given-names: Mihaly
  email: kolmisi@gmail.com

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