---
title: "FAQ"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{FAQ}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

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


Here are answers to some common questions about **ade4** (more to come soon).

## Installation

### How to install the current version of `ade4`?
The easiest way to install ade4 is to use `install.packages("ade4")` in your R session.

### How to install the development version of `ade4`?
To install the development version from github:

```r
remotes::install_github("adeverse/ade4")
```

### How do I know which `ade4` version I'm using?
In your R session, type:

```r
packageDescription("ade4", field="Version")
```

## Graphics

### What is `adegraphics`?
The package `adegraphics` provides a complete reimplementation of graphical functionalities of `ade4`. It is based on `lattice` and provides a convenient way to manage graphics as objects. Moreover, it offers much more flexibility than `ade4` to customize your plots.

### How to load `adegraphics`?
As `adegraphics` provides a reimplementation of `ade4` graphical functions, many functions have the same name in the two packages. To be sure to use `adegraphics` functions, `adegraphics` should be loaded **after** `ade4`:

```{r, message=FALSE}
library(ade4)
library(adegraphics)
```

An alternative it to explicitly specify the package in the call using the `::` operator:

```{r, eval=FALSE}
adegraphics::s.label()
```


### How to interpret ellipses plotted by `s.class` function?
The ellipses represent the main variation for individuals of a given class. They are based on inertia statistics not on significance levels.

## Simple Analysis
### How to obtain coordinates for individuals?
In simple analysis (e.g., `dudi.pca`), scores for individuals are stored in `$li` element of the returned object

### How to obtain coordinates for variables?
In simple analysis (e.g., `dudi.pca`), scores for variables are stored in `$co` element of the returned object

### What are the `$l1` and `$c1` elements of a dudi ?
In simple analysis (e.g., `dudi.pca`), the `$c1` element contains the principal axes (aka "loadings" of the variables) and the `$l1` element contains the principal components. The norm of these two elements is equal to 1, which makes them useful for drawing biplots (for example).