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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(collapse = TRUE,
comment = "#>",
fig.path = "man/figures/",
out.width = "100%")
```
## :mortar_board: Practice 2 - Rmarkdown
<!-- badges: start -->
[](https://choosealicense.com/licenses/gpl-2.0/)
<!-- badges: end -->
Structure of the research compendium of the [practice 2](https://rdatatoolbox.github.io/ex-rmarkdown.html) of the training course
[**Reproducible Research in Computational Ecology**](https://rdatatoolbox.github.io/).
### Content
This repository is structured as follow:
- [`data/`](https://github.com/rdatatoolbox/practice2/tree/main/data):
contains all raw data required to perform analyses
- [`R/`](https://github.com/rdatatoolbox/practice2/tree/main/R):
contains R functions developed especially for this project
- [`man/`](https://github.com/rdatatoolbox/practice2/tree/main/man):
contains help files of R functions
- [`DESCRIPTION`](https://github.com/rdatatoolbox/practice2/tree/main/DESCRIPTION):
contains project metadata (author, date, dependencies, etc.)
- [`index.Rmd`](https://github.com/rdatatoolbox/practice2/tree/main/index.Rmd):
contains the entire analysis
- [`make.R`](https://github.com/rdatatoolbox/practice2/tree/main/make.R):
main R script to run the entire project by rendering the [`index.Rmd`](https://github.com/rdatatoolbox/practice2/tree/main/index.Rmd)
### Usage
Fork and clone the repository, open R/RStudio and run:
```{r eval = FALSE}
source("make.R")
```
The final result is [`index.html`](https://github.com/rdatatoolbox/practice2/tree/main/index.html) and it is
available online [here](https://rdatatoolbox.github.io/practice2).
### Notes
- All required packages, listed in the `DESCRIPTION` file, will be installed (if necessary)
- All required packages and R functions will be loaded
### How to cite
> Casajus N, Bonnici I, Dray S, Gimenez O, Guéry L, Guilhaumon F, Schiettekatte NMD & Siberchicot A (2023) Workshop FRB-CESAB & RT EcoStat: Reproducible Research in Computational Ecology. Zenodo. <http://doi.org/10.5281/zenodo.4262978>.