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---
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output: github_document
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---

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# RLA paper <img src="data/logo_RLA/RLA_logo_2.png" align="right" width="120"/>

<br>
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```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

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# Presentation
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This repository stores all scripts and results of the RLA paper which is being published in Frontiers in Marine science. It records all the work made but also can be used as a reproducible repository for whom want to redo, improve or test analyses.
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![](data/readme_files/paper_screenshot.png)

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## Prerequisites
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It is necessary to install {RLA} package, to do so :
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```{r eval=FALSE}
install.packages("remotes")
remotes::install_gitlab(
  host = "https://gitlab.univ-lr.fr",
  repo = "pelaverse/rla"
)
library(RLA)

```

# Organisation of the repository

2 main part can be considered :
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-   PBR analysis : The scripts to perform the PBR analyses are stored at : [script/PBR](script/PBR)
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-   RLA analysis :
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    -   All output of RLA scenarios performed on supercomputer are stored as **RData** files at : [res/RLA](res/RLA)
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    -   These output can be analysed using script [R/Thor/03_AnalyseOutput.r](R/Thor/03_AnalyseOutput.r)
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# Case studies application

The two case studies cited in the paper are presented shiny application. Results of each scenarios tested are presented with graphical illustration.

-   For the PBR shiny application on small delphinide : <https://gitlab.univ-lr.fr/pelaverse/pbrfrtuning>

-   For the RLA shiny application on Harbour porpoise : <https://gitlab.univ-lr.fr/pelaverse/rlascenarioviz>