epiversetraceworkshop

The Title of the Project

https://github.com/emprestige/epiversetraceworkshop

Repository

The Title of the Project

README.Rmd

---
output: github_document
---




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



# EpiverseTraceWorkshop






Research Compendium of the project, here we provide a sample README file to practice reproducible coding.



## How to cite

Please cite this compendium as: 

```{r, echo = FALSE}
readCitationFile(file = "inst/CITATION")
```



## Content

This repository is structured as follow:

- [`data/`](https://github.com/emiel200/EpiverseTraceWorkshop/tree/master/data):
contains all raw data required to perform analyses

- [`analyses/`](https://github.com/emiel200/EpiverseTraceWorkshop/tree/main/analyses/):
contains R scripts to run each step of the workflow

- [`outputs/`](https://github.com/emiel200/EpiverseTraceWorkshop/tree/main/outputs):
contains all the results created during the workflow

- [`figures/`](https://github.com/emiel200/EpiverseTraceWorkshop/tree/main/figures):
contains all the figures created during the workflow

- [`R/`](https://github.com/emiel200/EpiverseTraceWorkshop/tree/main/R):
contains R functions developed especially for this project

- [`man/`](https://github.com/emiel200/EpiverseTraceWorkshop/tree/main/man):
contains help files of R functions

- [`DESCRIPTION`](https://github.com/emiel200/EpiverseTraceWorkshop/tree/main/DESCRIPTION):
contains project metadata (author, date, dependencies, etc.)

- [`make.R`](https://github.com/emiel200/EpiverseTraceWorkshop/tree/main/make.R):
main R script to run the entire project by calling each R script stored in the `analyses/` folder


## Usage

First, clone this repository. You can follow [steps on creating a new Rstudio Project from a GitHub repository](https://www.epirhandbook.com/en/version-control-and-collaboration-with-git-and-github.html?q=clone#clone-from-a-github-repository). 

Then, 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


## Licenses

**Text and figures :**  [CC-BY-4.0](http://creativecommons.org/licenses/by/4.0/)

**Code :** See the [DESCRIPTION](DESCRIPTION) file

**Data :** [CC-0](http://creativecommons.org/publicdomain/zero/1.0/) attribution requested in reuse


## 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.

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 "EpiverseTraceWorkshop" in publications use:'
type: software
license: GPL-2.0-or-later
title: 'EpiverseTraceWorkshop: My Reproducable Project'
version: 0.0.0.9000
abstract: A paragraph providing a full description of the project (on several lines...)
authors:
- family-names: Prestige
  given-names: Em
  email: emiel200@gmail.com
  orcid: https://orcid.org/orcid
preferred-citation:
  type: generic
  title: 'EpiverseTraceWorkshop: My Reproducable Project'
  authors:
  - family-names: Prestige
    given-names: Em
    email: emiel200@gmail.com
    orcid: https://orcid.org/orcid
  url: https://github.com/emiel200/EpiverseTraceWorkshop
  abstract: A paragraph providing a full description of the project (on several lines...)
  year: '2023'
  version: 0.0.0.9000
repository-code: https://github.com/emiel200/EpiverseTraceWorkshop
url: https://github.com/emiel200/EpiverseTraceWorkshop
contact:
- family-names: Prestige
  given-names: Em
  email: emiel200@gmail.com
  orcid: https://orcid.org/orcid

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