---
title: "Introduction: installing and citing Haplin"
author: "Hakon K. Gjessing and Julia Romanowska"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
%\VignetteEngine{knitr::rmarkdown}
%\VignetteIndexEntry{Introduction: installing and citing Haplin}
%\VignetteEncoding{UTF-8}
---
# Citing use of Haplin
If you find Haplin useful, please acknowledge our work by citing:
> Gjessing HK and Lie RT. ["Case-parent triads: Estimating single- and double-dose effects of fetal and maternal disease gene haplotypes."](https://haplin.bitbucket.io/docu/Gjessing_Lie_2006.pdf) __Annals of Human Genetics__ _(2006)_ 70, pp. 382-396.
The BibTex entry for LaTeX users can be obtained by the following command in R:
```{r echo=FALSE,results='hide',message=FALSE,warning=FALSE}
library( Haplin, quietly = TRUE )
```
```{r }
citation( "Haplin" )
```
# Obtaining and installing Haplin
## Requirements
Haplin is written for use with the statistical software R. However, it is easy to install and requires no previous knowledge of R. R can be downloaded free of charge from [The R Project for Statistical Computing](https://www.r-project.org/). Haplin is implemented as a standard R library, and should run without problems on all reasonably new R versions, for Windows, Linux or MAC.
Haplin is dependent on several other R packages:
`MASS, mgcv, tools, ff, ffbase, snow`
These are automatically installed together with Haplin (see below).
If you are using Windows, you should install [RTools](https://cran.r-project.org/bin/windows/Rtools/) before installing Haplin in R. RTools include the __zip__ command, which is required by the __ff__ package.
Moreover, if you want to use the plotting functions for plotting the results of __haplinSlide__ and __haplinStrat__, you should install the [ggplot2](https://CRAN.R-project.org/package=ggplot2) package separately. You can still use Haplin if you don't have this package, though!
For running on a cluster, you would need the [Rmpi](https://CRAN.R-project.org/package=Rmpi) package installed, see the vignette __"Running Haplin on cluster"__.
## Installation
To install Haplin in R:
```{r eval=FALSE}
install.packages( "Haplin", dependencies = TRUE )
```
Haplin and the dependent packages will then be installed automatically over the internet from the [CRAN library](https://CRAN.R-project.org/package=Haplin).
To start using Haplin, open a new R session (either in a terminal window or any IDE, e.g., [RStudio](https://posit.co/)). Then, use the R command:
```{r eval=FALSE}
library( Haplin )
```
Haplin is then loaded and ready for use.