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https://github.com/avallecam/rcompendiumtest5
:package: The Title of the Project
https://github.com/avallecam/rcompendiumtest5
Last synced: 1 day ago
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:package: The Title of the Project
- Host: GitHub
- URL: https://github.com/avallecam/rcompendiumtest5
- Owner: avallecam
- License: gpl-2.0
- Created: 2023-08-15T17:36:12.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2023-08-25T19:10:13.000Z (about 1 year ago)
- Last Synced: 2023-08-25T23:52:45.059Z (about 1 year ago)
- Language: R
- Homepage: https://avallecam.github.io/rcompendiumtest5/
- Size: 453 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE.md
- Code of conduct: .github/CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(collapse = TRUE,
comment = "#>",
fig.path = "man/figures/",
out.width = "100%")
```
# rcompendiumtest5
[](https://choosealicense.com/licenses/gpl-2.0/)
[](#)
Research Compendium of the project on Open, Reproducible and Sustainable code for epidemic analysis with R packages.
### How to cite
Please cite this compendium as in [Citing rcompendiumtest5](https://avallecam.github.io/rcompendiumtest5/authors.html#citation).
```{r,echo=FALSE}
cat(pkgdown:::data_citations()$html)
```
```{r,echo=FALSE}
cat(pkgdown:::data_citations()$bibtex)
```
```{r}
utils::readCitationFile(file = "inst/CITATION",
meta = packageDescription("cffr"))
```
### Content
This repository is structured as follow:
- [`data/`](https://github.com/avallecam/rcompendiumtest5/tree/master/data):
contains all raw data required to perform analyses
- [`analyses/`](https://github.com/avallecam/rcompendiumtest5/tree/main/analyses/):
contains R scripts to run each step of the workflow
- [`outputs/`](https://github.com/avallecam/rcompendiumtest5/tree/main/outputs):
contains all the results created during the workflow
- [`figures/`](https://github.com/avallecam/rcompendiumtest5/tree/main/figures):
contains all the figures created during the workflow
- [`R/`](https://github.com/avallecam/rcompendiumtest5/tree/main/R):
contains R functions developed especially for this project
- [`man/`](https://github.com/avallecam/rcompendiumtest5/tree/main/man):
contains help files of R functions
- [`DESCRIPTION`](https://github.com/avallecam/rcompendiumtest5/tree/main/DESCRIPTION):
contains project metadata (author, date, dependencies, etc.)
- [`make.R`](https://github.com/avallecam/rcompendiumtest5/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 the repository](https://www.epirhandbook.com/en/version-control-and-collaboration-with-git-and-github.html?q=clone#clone-from-a-github-repository). Then, to reproduce all the outputs, 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