t3

Tropical Tuna Treatment

https://github.com/ob7-ird/t3

Keywords

Repository

Tropical Tuna Treatment

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
options(tibble.print_min = 5, tibble.print_max = 5)
```

# t3 package 


[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/t3)](https://cran.r-project.org/package=t3)
[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
[![DOI](https://zenodo.org/badge/210599699.svg)](https://zenodo.org/badge/latestdoi/210599699)
[![R-CMD-check](https://github.com/OB7-IRD/t3/workflows/R-CMD-check/badge.svg)](https://github.com/OB7-IRD/t3/actions)


***Tropical Tuna Treatment***

## Warning
Package and documentation still in construction ! We need few more time to reach 88 miles per hours, be patient.

## Overview

The new version of Tropical Tuna Treatment (T3) process is developed in R language and available through a package. One of the advantages of this language is that it is more understandable and manipulated by the fisheries’ scientific community rather than Java language. Moreover, this development follows the principles of the open and reproducible science:

* Process transparency: the code is fully documented and the [documentation](https://ob7-ird.github.io/t3) of how works the program will be available.
* Open access and Open source: the code source is hosted on a github repository [t3](https://github.com/OB7-IRD/t3/) under a GPL version 3 license. In the end, it would be available on the Comprehensive R Archive Network (CRAN).
* Referencing of the software enable result reproducibility and versioning: version 2.0.1 [DOI: 10.5281/zenodo.14947393](https://zenodo.org/badge/latestdoi/210599699).

## Installation

```{r install, eval = FALSE}
devtools::install_github("https://github.com/OB7-IRD/t3")
```

### Development version

To get a bug fix or to use a feature from the development version, you can install the development version of t3 from GitHub.

```{r install_dev, eval = FALSE}
devtools::install_github("https://github.com/OB7-IRD/t3",
                         ref = "development")
```

## Cheatsheet

Working in progress for this section. Be patient.

## Usage

```{r library, eval=FALSE, message = FALSE}
library(t3)
```

Several examples of processes are available in the section [Running processes examples](https://ob7-ird.github.io/t3/articles/running_processes_examples.html).

## Getting help

If you encounter a clear bug, please file an issue with a minimal reproducible example on [GitHub issues page](https://github.com/OB7-IRD/t3/issues). This link is also available if you have any questions and improvement propositions.

## References

Working in progress for this section.

Owner

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "t3" in publications use:'
type: software
license: GPL-3.0-only
title: 't3: Tropical Tuna Treatment'
version: 2.1.2
doi: 10.5281/zenodo.3878124
abstract: The multi-species nature of tropical tuna surface fisheries highlights a
  series of difficulties when catches are estimated by species and size statistics.
  The Tropical Tuna Treatment (T3) process was initiated more than 30 years ago and
  is still today the result of a strong collaboration between several countries (notably
  France, Spain, the Seychelles and Senegal). Is aims are to correct biases of the
  logbook data on species composition and provide more accurate catch estimations
  per species for the purse seiner fleet, especially European and Seychelles fleet.
authors:
- family-names: Clément
  given-names: Jeanne
  email: jeanne.clement@ird.fr
  orcid: https://orcid.org/0000-0002-5228-5015
- family-names: Depetris
  given-names: Mathieu
  email: mathieu.depetris@ird.fr
  orcid: https://orcid.org/0000-0001-8080-0531
- family-names: Duparc
  given-names: Antoine
  email: antoine.duparc@ird.fr
  orcid: https://orcid.org/0000-0001-6135-9015
- family-names: Cauquil
  given-names: Pascal
  email: pascal.cauquil@ird.fr
  orcid: https://orcid.org/0000-0003-0718-8950
- family-names: Floc'h
  given-names: Laurent
  email: laurent.floch@ird.fr
  orcid: https://orcid.org/0000-0003-4764-9766
- family-names: Lebranchu
  given-names: Julien
  email: julien.lebranchu@ird.fr
  orcid: https://orcid.org/0000-0002-7759-0534
repository-code: https://github.com/OB7-IRD/t3
url: https://zenodo.org/badge/latestdoi/210599699
date-released: '2025-04-14'
contact:
- family-names: Clément
  given-names: Jeanne
  email: jeanne.clement@ird.fr
  orcid: https://orcid.org/0000-0002-5228-5015
keywords:
- pkgdown
- r
- t3-project

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