index.Rmd

---
title: "Biodose Tools"
subtitle: "User Manual & Documentation"
author: "Alfredo Hernández, Joan Francesc Barquinero"
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
output: bookdown::bs4_book
documentclass: scrartcl
bibliography: [bib/articles.bib, bib/manuals.bib, bib/software.bib, bib/packages.bib, bib/extra.bib]
biblio-style: abbrv
# biblio-style: apalike
link-citations: yes
github-repo: biodosetools-team/documentation
description: "User Guide & Documentation for Biodose Tools"
apple-touch-icon: "favicon-highres.png"
apple-touch-icon-size: 120
favicon: "favicon.png"
cover-image: "images/cover.png"
---


# Welcome {-}

```{r setup, include=FALSE}
library(dplyr)
library(biodosetools)
options(knitr.graphics.auto_pdf = TRUE)

source("contents/aux_functions.R")
```

```{r echo=FALSE, out.width = '60%', fig.align='center'}
knitr::include_graphics("images/home.svg")
```

[Biodose Tools](https://biodosetools-team.github.io/biodosetools/) ([Hernández et al. 2023](https://doi.org/10.1080/09553002.2023.2176564)) is an open source project that aims to be a tool to perform all different tests and calculations needed by biological dosimetry laboratories. The app is developed using the [R](https://www.r-project.org/about.html) [@R-base] programming language and [Shiny](https://shiny.rstudio.com/) [@R-shiny] as a framework to offer an online, easy-to-use solution. Although the intention is to provide the application as a website, all R routines are available as an R package, which can be downloaded for improvement or personal use.

We also aim to clarify and explain the tests used and to propose those considered most appropriate. Each laboratory in its routine work should choose the most suitable method, but the project aims to reach a consensus that will help us in case of mutual assistance or intercomparisons.

The project is initially developed by [RENEB](https://www.reneb.net/) association, but contributions are always welcome.

```{r, echo = FALSE, out.width = '15%', fig.align = "center"}
knitr::include_graphics("images/cc-by-nc-sa.png", dpi = 192)
```

The online version of this book is licensed under the [Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License](http://creativecommons.org/licenses/by-nc-sa/4.0/).

```{r include=FALSE}
# Automatically create a bib database for R packages
knitr::write_bib(c(
  .packages(),
  # Markdown
  "bookdown", "knitr", "rmarkdown", "markdown",
  # R API
  "tidyverse", "dplyr", "tidyr", "rlang", "ggplot2", "magrittr",
  "stats", "MASS", "maxLik", "mixtools", "msm", "cli",
  # Shiny
  "shiny", "shinydashboard", "shinyWidgets", "bsplus",
  "rhandsontable", "pander", "xtable",
  # Golem
  "config", "golem"
), "bib/packages.bib")
```